WO2023196869A1 - Anticorps anti-epha2 - Google Patents

Anticorps anti-epha2 Download PDF

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Publication number
WO2023196869A1
WO2023196869A1 PCT/US2023/065395 US2023065395W WO2023196869A1 WO 2023196869 A1 WO2023196869 A1 WO 2023196869A1 US 2023065395 W US2023065395 W US 2023065395W WO 2023196869 A1 WO2023196869 A1 WO 2023196869A1
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seq
antibody
region
sequence
amino acid
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PCT/US2023/065395
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Alexander Scholz
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Atreca, Inc.
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Publication of WO2023196869A1 publication Critical patent/WO2023196869A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2866—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for cytokines, lymphokines, interferons
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A61K47/68031—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates the drug being an auristatin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6849—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a receptor, a cell surface antigen or a cell surface determinant
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6889—Conjugates wherein the antibody being the modifying agent and wherein the linker, binder or spacer confers particular properties to the conjugates, e.g. peptidic enzyme-labile linkers or acid-labile linkers, providing for an acid-labile immuno conjugate wherein the drug may be released from its antibody conjugated part in an acidic, e.g. tumoural or environment
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2878—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/54—Medicinal preparations containing antigens or antibodies characterised by the route of administration
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/35—Valency
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
    • C07K2317/732—Antibody-dependent cellular cytotoxicity [ADCC]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/75—Agonist effect on antigen
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/10—Protein-tyrosine kinases (2.7.10)
    • C12Y207/10001—Receptor protein-tyrosine kinase (2.7.10.1)

Definitions

  • EPHA2 ANTIBODIES RELATED APPLICATIONS [0001] This application claims priority to U.S. Application No.63/362,476, filed on April 5, 2022, and U.S. Application No.63/374,797, filed on September 7, 2022. The entire content of each provisional application is herein incorporated by reference for all purposes.
  • REFERENCE TO SEQUENCE LISTING [0002] The Sequence Listing .xml file, identified as 097519-1374172-2901 PCT, is 11,32,370 bytes in size and was created on March 28, 2023. The Sequence Listing is hereby incorporated by reference in its entirety.
  • FIELD OF CANCER THERAPEUTICS [0003] This application relates to therapeutic antibodies for the treatment of various cancers.
  • EphA2 is a tyrosine kinase and belongs to the family of Ephrin receptors. Like other Ephrin receptors, it is a single-pass membrane protein with large extracellular N-termini. EphA2 is typically involved in cell-cell repulsion or adhesion processes. EphA2 is also known to promote angiogenesis. EphA2 is overexpressed in tumor tissues compared to normal adult tissues, indicating its potential application in cancer treatment. Although several EphA2 antibodies have been developed, some of which are being assessed in clinical trials, these antibodies have the shortcomings of high toxicity and insufficient efficacy. They are unable to meet the needs of cancer patients.
  • an immunoconjugate comprising an antibody that binds to ephrin receptor A2 (EphA2) and a cytotoxic agent, wherein the cytotoxic agent is an auristatin analogue, and wherein the antibody is conjugated to the auristatin analogue.
  • EphA2 ephrin receptor A2
  • the auristatin analogue has a formula of: [0006]
  • the linker has a formula of wherein: Z is a linking group that joins the linker to a target group on the antibody; Str is a stretcher; AA 1 and AA 2 are each independently an amino acid, wherein AA 1 -[AA 2 ] r forms a protease cleavage site; X is a self-immolative group; s is 0 or 1; m is 1, 2, 3 or 4; o is 0, 1 or 2; # is the point of attachment to the antibody, and % is the point of attachment to the auristatin analogue.
  • the immunoconjugate has a formula of: wherein: L is a cleavable linker; n is the drug-to-antibody ratio (DAR) and is an integer from 1 to 12, and Ab is the antibody. [0008] In some embodiments, the immunoconjugate has a formula of:
  • n is the drug-to-antibody ratio (DAR) and is an integer from 1 to 12, and Ab is the antibody.
  • the antibody of the immunoconjugate binds to an epitope of EphA2 located in the FN2 domain of EphA2, wherein the FN2 domain has the sequence of TEPPKVRLEGRSTTSLSVSWSIPPPQQSRVWKYEVTYRKKGDSNSYNVRRTEGFSV TLDDLAPDTTYLVQVQALTQEGQGAGSKVHEFQTLSPEGSGN (SEQ ID NO: 95).
  • the epitope comprises at least one, at least two, at least three, at least four, at least five, or at least six, at least seven, at least eight, or at least nine, or all ten of amino acid residues Leu444, Arg447, Lys476, Gln506, Ser519, Lys520, Val521, Glu523, Phe524, and Gln525 of SEQ ID NO: 94.
  • the antibody of the immunoconjugate has one or more properties of: a) activates the ephrin A1-EphA2 signaling axis at least 95%, 90%, 85%, or 80% less than ephrin-A1 activates the ephrin A1-EphA2 signaling axis, b) binds preferentially to a tumor tissue than normal tissue, c) has an EC 50 for activation of the ephrinA1-EphA2 signaling axis that is at least 10-, 20-, 50-, 100-, 200-, 500-fold less potent than the ADCC EC 50 of the antibody; and /or d) has ADCP activity, and e) has ADCC activity.
  • the antibody of the immunoconjugate disclosed herein binds to a tumor tissue preferentially compared to normal tissue.
  • the antibody of the immunoconjugate comprises a heavy chain variable region comprising: an HCDR1 of any one of SEQ ID NOS:1-11 and 201-265 or a variant thereof in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence; an HCDR2 of any one of SEQ ID NOS:12-22 and 266-330 or a variant thereof in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence; and an HCDR3 of any one of SEQ ID NOS:23-33 and 331-395 or a variant thereof in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence; a light chain variable region comprising: an LCDR1 of any one of SEQ ID NOS:34-44 and 396-460 or a variant thereof in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence; an LCDR2
  • the antibody of the immunoconjugate comprises a heavy chain variable region comprising: an HCDR1 comprising a sequence (SEQ ID NO:1) or a variant HCDR1 in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence; an HCDR2 comprising a sequence (SEQ ID NO:12), or a variant HCDR2 in which 1, 2, 3, 4, or 5 amino acids substituted relative to the sequence; and an HCDR3 comprising a sequence (SEQ ID NO:23), or a variant HCDR3 in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence.
  • the antibody further comprises a light chain variable region comprising: an LCDR1 comprising a sequence (SEQ ID NO:34) or a variant LCDR1 in which 1, 2, 3, 4, or 5 amino acids is substituted relative to the sequence; an LCDR2 comprising a sequence (SEQ ID NO:45), or variant LCDR2 in which 1, 2, or 3 amino acids is substituted relative to the sequence; and an LCDR3 comprising a sequence (SEQ ID NO:56), or a variant LCDR3 in which 1, 2, 3, 4, or 5 amino acids is substituted relative to the sequence.
  • the antibody of the immunoconjugate comprises: (a) an HCDR1 sequence of GGSX 1 X 2 X 3 YX 4 WS where X 1 is F or L, X 2 is S or N, X 3 is D or G, and X 4 is Y or H (SEQ ID NO: 769); (b) an HCDR2 sequence of EX 1 NHX 2 GSX 3 X 4 YNNYNPSLKS, where X 1 is I or V, X 2 is A, Q, R or S, X 3 is I or T, and X 4 is N or S (SEQ ID NO: 770); (c) an HCDR3 sequence of AKPX 1 RPHC X 2 NGVCX 3 SGDAFDI, where X 1 is L or F, X 2 is I or T; and X 3 is Y or S (SEQ ID NO: 771); (d) an LCDR1 sequence of X 1 GNNIGX 2 X 3 X
  • the antibody of the immunoconjugate comprises: (a) an HCDR1 sequence of GGSX 1 X 2 X 3 YX 4 WS where X 1 is F or L, X 2 is S or N, and X 3 is D or G, and X 4 is Y or H (SEQ ID NO: 769); (b) an HCDR2 sequence of EX 1 NHX 2 GSX 3 X 4 YNPSLKS, where X 1 is I or V, X 2 is A, Q, R or S, X 3 is I or T, and X 4 is N or S (SEQ ID NO: 774); (c) an HCDR3 sequence of AKPX 1 RPHCX 2 NGVCX 3 SGDAFDI, where X 1 is L or F, X 2 is I or T; and X 3 is Y or S (SEQ ID NO: 771); (d) an LCDR1 sequence of X 1 GNNIGX 2 X 3 X 4 V
  • the antibody comprises:(a) an HCDR1 sequence of GGSX 1 X 2 DYX 3 WS where X 1 is F or L, X 2 is S or N, and X 3 is Y or H (SEQ ID NO: 775); (b) an HCDR2 sequence of EX1NHX2 GS X3 X4YNPSLKS, where X1 is I or V, X2 is R or S, X3 is I or T, and X 4 is N or S (SEQ ID NO: 775); or an HCDR2 sequence of EX 1 NHX 2 GS X 3 X 4 YNNYNPSLKS, where X 1 is I or V, X 2 is R or S, X 3 is I or T, and X 4 N or S(SEQ ID NO: 777); and (c) an HCDR3 sequence of AKP X 1 RPHCTNGVCX2SGDAFDI, where X 1 is L or F and X 2
  • the antibody of the immunoconjugate comprises a V H comprising an amino acid sequence having at least 95% identity to a V H in Table 8; and a V L comprising an amino sequence having at 95% identity to a V L in Table 8.
  • the V H comprises an amino acid sequence having at least 95% identity to (SEQ ID NO: 67); and the VL comprises an amino sequence having at 95% identity to (SEQ ID NO: 78).
  • the V H comprises an amino acid sequence having at least 95% identity to a V H of any one of SEQ ID NOS:67-77 and 591- 655.
  • the V L comprises an amino sequence having at 95% identity to a V L of any one of SEQ ID NOS:78-88 and 656-720.
  • the antibody of the immunoconjugate comprises: a V H region comprising amino acid sequence SEQ ID NO:67 and a V L region comprising amino acid sequence SEQ ID NO:78; a V H region comprising amino acid sequence SEQ ID NO:68 and a V L region comprising amino acid sequence SEQ ID NO:79; a V H region comprising amino acid sequence SEQ ID NO:69 and a VL region comprising amino acid sequence SEQ ID NO:80; a V H region comprising amino acid sequence SEQ ID NO:70 and a VL region comprising amino acid sequence SEQ ID NO:81; a V H region comprising amino acid sequence SEQ ID NO:71 and a V L region comprising amino acid sequence SEQ ID NO:82; a V H region comprising amino acid sequence SEQ ID NO:72 and a V L region comprising amino acid sequence SEQ ID NO:
  • antibody of the immunoconjugate comprises: (1) a heavy chain variable (V H ) region and a light chain variable (V L ) region, wherein: (a) the V H region has at least 70% identity to SEQ ID NO:67; and comprises a CDR1 of SEQ ID NO:1, or the CDR1 of SEQ ID NO:1 in which 1, 2, 3, 4, or 5 amino acids are substituted; a CDR2 of SEQ ID NO:12, or the CDR2 of SEQ ID NO:12 in which 1, 2, 3, 4, or 5 amino acids are substituted; a CDR3 of SEQ ID NO:23 or the CDR3 of SEQ ID NO:23 in which 1, 2, 3, 4, or 5 are substituted; and (b) the V L region has at least 70% identity to SEQ ID NO: 78, and comprises a CDR1 of SEQ ID NO:34 or the CDR1 of SEQ ID NO:34 in which 1, 2, 3, 4, or 5 amino acids are substituted; a CDR2 of SEQ ID NO:45
  • the antibody comprises: a heavy chain variable (VH) region and a light chain variable (VL) region, (i) wherein the VH region has at least 70% identity to SEQ ID NO:67 and comprises (a) an HCDR1 sequence of GGSX1X2DYX3WS where X1 is F or L, X2 is S or N, and X3 is Y or H (SEQ ID NO: 775); (b) an HCDR2 sequence of EX1NHX2 GS X3 X4YNPSLKS, where X1 is I or V, X2 is R or S, X3 is I or T, and X4 is N or S (SEQ ID NO: 776); or an HCDR2 sequence of EX1NHX2 GS X3 X4YNNYNPSLKS, where X1 is I or V, X2 is R or S, X3 is I or T, and X4 N or S
  • the antibody of the immunoconjugate comprises an HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 of an antibody designated as AB-008873; AB-009805; AB- 009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB- 010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB-010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB-010364, AB-010365, AB- 01
  • the antibody of the immunoconjugate comprises a heavy chain variable region and a light chain variable region of an antibody designated as AB-008873; AB-009805; AB-009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB- 009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB-010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB- 010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB-010364, AB-010365, AB-010366, AB-010367, AB
  • the antibody of the immunoconjugate comprises a V H region of any one of SEQ ID NO 67-77 and 591-655, and/or a V L region of any one of SEQ ID NO: 78-88 and 656- 720, or an antibody comprising a V H region with at least 80% identity to any one of SEQ ID NO 67-77 and 591-655 and a V L region having at least 80% identity to any one of SEQ ID NO: 78-88 and 656- 720, with variations to the corresponding V H or V L regions present only in Framework regions.
  • the antibody of the immunoconjugate comprises an HCDR1 of any one of SEQ ID NOS:1-11, and 201-265, an HCDR2 of any one of SEQ ID NOS:12-22 and 266-330, an HCDR3 of any one of SEQ ID NOS:23-33 and 331-395, an LCDR1 of any one of SEQ ID NOS:34-44 and 396-460, an LCDR2 of any one of SEQ ID NOS:45-55 and 461-525, an LCDR3 of any one of SEQ ID NOS:56-66 and 526-590, wherein the FW regions in the V H region are at least 80% identical to the FW regions present in the V H region of SEQ ID NO 67-77 and 591-655, and wherein the FW regions in the V L region are at least 80% identical to the FW regions present in the V L region of SEQ ID NO: 78-88 and 656-720.
  • the antibody of the immunoconjugate is a non-natural antibody.
  • the antibody is a bispecific antibody comprising two antigen binding fragments, one binding to EphA2, and the other binds to a different antigen.
  • the different antigen is 4-1bb or CD3.
  • the immunoconjugate comprising the antibody disclosed herein further comprises one or more of an IL-15 receptor agonist, a TGF ⁇ trap, a TLR agonist, or a 4-1BB ligand (4- 1BBL).
  • a pharmaceutical composition comprising any of the immunoconjugates disclosed herein and a pharmaceutically acceptable carrier.
  • a method of inducing an immune response and/or treating cancer comprising administering any one of the immunoconjugates disclosed herein.
  • the immune response comprises an antibody-dependent cellular cytotoxicity (ADCC) and/or antibody dependent cellular phagocytosis (ADCP).
  • ADCC antibody-dependent cellular cytotoxicity
  • ADCP antibody dependent cellular phagocytosis
  • the antibody is administered intravenously.
  • a method of treating a cancer patient having a tumor overexpressing EphA2 the method comprising administering any one of the immunoconjugates disclosed herein to the patient.
  • the cancer is a gastric cancer, ovarian cancer, soft tissue sarcoma, lung cancer, head and neck cancer, uterine cancer, breast cancer, colorectal cancer, esophageal cancer, stomach cancer, kidney cancer, melanoma, liver cancer, bladder cancer, or testicular cancer.
  • the cancer is non-small cell lung cancer, triple-negative breast cancer, colorectal cancer, ovarian cancer or melanoma.
  • the method further comprises administering chemotherapy and/or radiation therapy.
  • the method comprises administering an agent that targets an immunological checkpoint antigen.
  • the agent is a monoclonal antibody.
  • the monoclonal antibody blocks PD-1 ligand binding to PD-1. In some embodiments, the monoclonal antibody is an anti-PD-1 antibody.
  • FIG.1 shows surface binding profile of AB-008873 in A549 cells and CT26 cells (in vitro and ex vivo).
  • FIG. 2A and FIG. 2B shows results of assessing the ADCC activity (FIG. 2A) and ADCP activity (FIG.2B) of AB-008873 in vitro functional assays.
  • FIG.3 shows the ADC activity of AB-008873 on in vitro cell lines.
  • FIG.4 compares the binding activity and functional activity of AB-008873 and other EphA2 antibodies on mouse and human cells.
  • FIG. 5A illustrates a method of octet in tandem binning for epitope mapping.
  • FIG. 5B illustrates the epitopes in the EphA2 domains recognized by EphA2 antibodies.
  • FIG.6 shows the results from a yeast display that demonstrates the binding of AB-008873 to FN2 of EphA2.
  • FIG.7 shows the design of an in vivo study to assess the effect of the AB-008873 treatment.
  • FIG.8 shows that AB-008873 treatment increased T cells in the blood.
  • FIG. 9 shows the effects on tumor growth of treatment of AB-008873 on mice inoculated with CT26 cells.
  • FIG.10 shows that AB-008873 treatment did not result in significant changes in TIL number.
  • FIG.11 shows that AB-008873 treatment did not significantly change T & NK cell numbers in the TME.
  • FIG.12 shows increased macrophage numbers in TME at Day 10 with 40 mg/kg AB-008873 treatment.
  • FIG.13 shows representative CD3+ CD8+ staining of cytotoxic T cells.
  • FIG.14 shows representative CD4+ FoxP3+ staining of regulatory T cells.
  • FIG.15 shows representative F4/80+ iNOS+ staining on M1 macrophages.
  • FIG.16 shows the effect of 40 mg/kg AB-008873 administered on tumor growth and body weight in mice inoculated with CT26 cells (murine colon carcinoma cells).
  • FIG. 17 shows flow cytometry analysis of total tumor-infiltrating leukocytes (TIL) and myeloid cells from tumors in mice inoculated with CT26 cells. The mice were treated with 40 mg/kg AB-008873 or PBS.
  • FIG. 18 shows flow cytometry analysis of lymphoid cells from tumors in mice inoculated with CT26 cells.
  • FIG. 19A, 19B, 19C, 19D, and 19E show results of activation of 4-1BB by EphA2-4-1BB bispecific antibodies in tumor cell lines.
  • FIG. 20 shows the functional activity of AB-008873 sibling antibodies (antibodies that are derived from the same lineage as AB-008873)
  • FIG. 21A-C show the functional activity of engineered AB-008873 variants: flow binding, ADC activity, and ADCC activity, respectively.
  • FIG.22 shows the reactivity of AB-010699 across a panel of human cancer samples.
  • FIG.23 shows the binding sites of various commercial EphA2 antibodies.
  • FIG.24 shows the reactivity of EphA2 antibodies across a panel of human cancer samples.
  • FIG.25 shows immunofluorescence study results demonstrating a possible unique epitope of AB-008873 in gastric cancer.
  • FIG.26 compares EphA2 antibodies in binding ovarian cancer and soft tissue sarcoma cells.
  • FIG.27 compares AB-008873 with commercial anti-EphA2 antibodies in binding to ovarian cancer and soft tissue sarcoma cells.
  • FIG. 28 compares the binding pattern of EphA2 antibodies in tumor tissues from different uterine cancer donors.
  • FIG.29 shows the binding pattern of EphA2 antibodies in tumor tissues from different head and neck cancer donors.
  • FIG.30 shows the binding pattern of EphA2 antibodies in tumor tissues from different Non- small Cell Lung cancer (NSCLC) donors.
  • FIG.31 shows the reactivity of EphA2 antibodies across a panel of additional human cancer samples.
  • FIG.32 shows schematics of the formats of multivalent antibodies, including the format of the Fc regions.
  • FIG.33 shows the binding of AB-008873, variants thereof, AB-010018 and commercial anti- EphA2 antibodies to normal kidney.
  • FIG.33 shows the binding of AB-008873, variants thereof, AB-010018 and commercial anti- EphA2 antibodies to normal kidney.
  • FIG. 34 shows the binding of AB-008873 and its variants, AB-010018, and a commercial anti-EphA2 antibody to a normal stomach.
  • FIG. 35 shows a comparison of the ADC activity of AB-008873 with AB-009815 (comprising an H76PT mutation relative to AB-008873). This mutation removes a medium-risk DP proteolytic cleavage site that could cause AB degradation in the serum, decreasing half-life after injection in mice/humans. The results showed that the ADC activity of AB-009815 is substantially similar to that of AB-008873 in H522, LoVo, A375, SKOV3, A549, and MDAMB231 cells.
  • FIG.36 is a schematic illustration of AB-008873-IL15 fusions.
  • FIG. 37 shows that AB-008873-IL15 multiMabs treatment resulted in dose-dependent increases in human NK cell proliferation.
  • FIG.38 shows the flow cytometry analysis of the binding of the AB-008873-IL15 multiMabs to tumor cells using flow cytometry.
  • FIG. 39A-D show alignments and CDR designations for various EphA2 antibodies.
  • FIG. 40 compares the ADCC activity of several of anti-EphA2 antibodies AB-010361 (“AB- 010361-15”), AB-010681 (“AB-010681-2”), and AB-010685 (“AB-010681-2”) on A549 cells.
  • FIG. 41 shows the results of thermostability analysis of the anti-EphA2 antibodies AB- 008873 and AB-010699.
  • FIG.42 shows immunofluorescence staining results of AB-008873 variants as compared to AB-008873, and AB-010018.
  • FIG. 43A and FIG. 43B show the phosphorylation of Y588 and S897 on EphA2 by anti- EphA2 antibodies AB-008873, AB-010361, AB-010699, AB-010016, AB-010018, and AB-010019 in agonist (FIG.43A) and antagonist (FIG.43B) assay.
  • FIG. 44 shows identification of AB-008873 epitope residues by yeast display.
  • FIG.45 shows the alignment of the epitope residues across the EphA/B family members. The results show that the residues are divergent across the EphA/B family and the epitope is conformational.
  • FIG.45 discloses SEQ ID NOS 783-827 and 829-838, respectively, in order of appearance. [0078] FIG.
  • FIG. 46 shows the alignment of the epitope residues across multiple species: human, cynomolgus monkey (“cyno”), mouse, and rat.
  • FIG. 46 discloses SEQ ID NOS 839-841 and 828, respectively, in order of appearance.
  • FIG. 47 illustrates the co-crystallization configuration of the EphA2 protein and the AB- 008873 antibody. It indicates that the HCDRs changes conformation upon binding to the EphA2 protein: the disulfide loop in HCDR3 shows substantial rotation as compared to the structure that is not in contact with EphA2.
  • FIG. 48 shows measurements of tumor growth in mice inoculated with CT26 cells upon treatment of the AB-008873-IL15. [0081] FIG.
  • FIG. 50A compares the cytotoxicity of AB-008873, AB-010361, AB-010699, and AB- 010018 on A549 cells.
  • FIG. 50B compares the cytotoxicity of AB-010699, AB-010695, AB-010363, AB-010699, and Cetuximab on A549 cells.
  • FIG.51 compares the cytotoxicity of AB-008873, AB-010361, and AB-010699 in an ADC assay.
  • FIG. 50A compares the cytotoxicity of AB-008873, AB-010361, and AB-010699 in an ADC assay.
  • FIG.53 shows representative anti-CD3 bispecific antibody constructs.
  • FIG.54 shows measurements of tumor growth of NSG-DKO mice carrying PC3 tumor cells upon treatment of a bispecific antibody comprised of AB-010361 and an anti-CD3 binding arm.
  • FIG. 55A-D show cytotoxicity results of antibody-drug conjugates, each comprising an EphA2 antibody, AB-010361 (IgG1), AB-010361 (IgG4), AB-10699 (IgG1), or AB-010671 (IgG1), directly conjugated to a ZymeLink Auristatin (ZLA) payload.
  • ZLA ZymeLink Auristatin
  • FIG. 57 shows endpoint tumor weight analysis of NPG mice carrying tumors established from PC3 cells upon treatment of ZLA-conjugated EphA2 antibodies.
  • FIG.58A-58D show the body weight analysis of NPG mice that carrying tumors established from PC3 cells upon treatment of ZLA-conjugated EphA2 antibodies.
  • FIG.59A shows cytotoxicity results on PC3 cells of AB-10699-IgG1, AB-10699-IgG4, AB- 010671-IgG1, and AB-010671-IgG4 directly conjugated to a ZymeLink Auristatin (ZLA) payload.
  • ZLA ZymeLink Auristatin
  • FIG. 60A shows measurements of tumor growth of NPG mice carrying PC3 tumor cells measuring ⁇ 150 mm 3 upon administration of AB-10699-IgG1, AB-10699-IgG4, AB-010671-IgG1, and AB-010671-IgG4 directly conjugated to a ZymeLink Auristatin (ZLA).
  • FIG. 60B shows the body weight of the mice over the course of the study. IgG1 and IgG4 isotype antibodies are included as controls.
  • FIG. 60A shows measurements of tumor growth of NPG mice carrying PC3 tumor cells measuring ⁇ 150 mm 3 upon administration of AB-10699-IgG1, AB-10699-IgG4, AB-010671-IgG1, and AB-010671-IgG4 directly conjugated to a ZymeLink Auristatin (ZLA).
  • FIG. 60B shows the body weight of the mice over the course of the study. IgG1 and IgG4 isotype antibodies are included as controls.
  • FIG. 61A shows measurements of tumor growth of NPG mice carrying PC3 tumor cells measuring ⁇ 400 mm 3 upon administration of AB-10699-IgG1, AB-10699-IgG4, AB-010671-IgG1, and AB-010671-IgG4 directly conjugated to a ZymeLink Auristatin (ZLA).
  • FIG. 61B shows the body weight of the mice over the course of the study. IgG1 and IgG4 isotype antibodies are included as controls.
  • DETAILED DESCRIPTION [0094] This application incorporates the entire disclosure of PCT publication WO 2022/187710 by reference for all purposes.
  • an antibody optionally includes a combination of two or more such molecules, and the like.
  • antibody means an isolated or recombinant binding agent that comprises the necessary variable region sequences to specifically bind an antigenic epitope.
  • an “antibody” as used herein is any form of antibody of any class or subclass or fragment thereof that exhibits the desired biological activity, e.g., binding a specific target antigen.
  • a monoclonal antibody including full-length monoclonal antibodies
  • human antibodies chimeric antibodies
  • nanobodies diabodies
  • multispecific antibodies e.g., bispecific antibodies
  • antibody fragments including but not limited to scFv, Fab, and the like so long as they exhibit the desired biological activity.
  • “Antibody fragments” comprise a portion of an intact antibody, for example, the antigen- binding or variable region of the intact antibody.
  • antibody fragments include Fab, Fab’, F(ab’) 2 , and Fv fragments; diabodies; linear antibodies (e.g., Zapata et al., Protein Eng.8(10): 1057- 1062 (1995)); single-chain antibody molecules (e.g., scFv); and multispecific antibodies formed from antibody fragments.
  • Papain digestion of antibodies produces two identical antigen-binding fragments, called “Fab” fragments, each with a single antigen-binding site, and a residual “Fc” fragment, a designation reflecting the ability to crystallize readily.
  • Pepsin treatment yields an F(ab’) 2 fragment with two antigen combining sites and is still capable of cross-linking antigen.
  • the term “targets a tumor,” or “tumor-targeting,” with respect to an antibody refers to an antibody that binds preferentially to a tumor tissue than normal tissue.
  • the normal tissue is the tissue that is adjacent to the tumor, referred to as tumor-adjacent tissue or TAT.
  • a tumor targeting antibody also decreases the rate of tumor growth, tumor size, invasion, and/or metastasis, via direct or indirect effects on tumor cells.
  • V-region refers to an antibody variable region domain comprising the segments of Framework 1, CDR1, Framework 2, CDR2, and Framework 3, including CDR3 and Framework 4.
  • the heavy chain V-region, V H is a consequence of rearrangement of a V-gene (HV), a D-gene (HD), and a J-gene (HJ), in what is termed V(D)J recombination during B-cell differentiation.
  • the light chain V-region, V L is a consequence of rearrangement of a V-gene (LV) and a J-gene (LJ).
  • CDR complementarity-determining region
  • the CDRs of each chain are referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also identified by the chain in which the CDR is located.
  • a V H CDR3 (HCDR3) is in the variable domain of the heavy chain of the antibody in which it is found
  • LCDR3 V L CDR3
  • CDR is used interchangeably with “HVR” in this application when referring to CDR sequences.
  • the amino acid sequences of the CDRs and framework regions can be determined using various well-known definitions in the art, e.g., Kabat, Chothia, international ImMunoGeneTics database (IMGT), and AbM (see, e.g., Chothia & Lesk, 1987, Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-917; Chothia C. et al., 1989, Conformations of immunoglobulin hypervariable regions. Nature 342, 877-883; Chothia C. et al., 1992, structural repertoire of the human V H segments J. Mol.
  • CDRs as shown in Tables 6 and 7 are defined by IMGT and Kabat.
  • the V H CDRs as listed in Table 6, are defined as follows: HCDR1 is defined by combining Kabat and IMGT; HCDR2 is defined by Kabat; and the HCDR3 is defined by IMGT.
  • the V L CDRs as listed in Table 7 are defined by Kabat.
  • a “nonlinear epitope” or “conformational epitope” comprises noncontiguous polypeptides (or amino acids) within the antigenic protein to which an antibody specific to the epitope binds.
  • a conformational epitope is typically formed by a three-dimensional interaction of amino acids in the epitope that may not necessarily be contained in a single stretch of amino acids.
  • an “Fc region” refers to the constant region of an antibody excluding the first constant region immunoglobulin domain.
  • Fc refers to the last two constant region immunoglobulin domains of IgA, IgD, and IgG, and the last three constant region immunoglobulin domains of IgE and IgM, and the flexible hinge N-terminal to these domains.
  • IgA and IgM Fc may include the J chain.
  • Fc comprises immunoglobulin domains C ⁇ 2 and C ⁇ 3 and the hinge between C ⁇ 1 and C ⁇ 2.
  • Fc region may vary, however, the human IgG heavy chain Fc region is usually defined to comprise residues C226 or P230 to its carboxyl-terminus, using the numbering according to the EU index as in Kabat et al. (1991, NIH Publication 91-3242, National Technical Information Service, Springfield, Va.).
  • the term “Fc region” may refer to this region in isolation or this region in the context of an antibody or antibody fragment. “Fc region” includes naturally occurring allelic variants of the Fc region as well as modified Fc regions, e.g., that are modified to modulate effector function or other properties such as pharmacokinetics, stability, or production properties of an antibody.
  • Fc regions also include variants that do not exhibit alterations in biological function.
  • one or more amino acids can be deleted from the N-terminus or C-terminus of the Fc region of an immunoglobulin without substantial loss of biological function.
  • Such variants can be selected according to general rules known in the art to have minimal effect on activity (see, e.g., Bowie et al., Science 247:306-1310, 1990).
  • a single amino acid substitution S228P according to Kabat numbering; designated IgG4Pro
  • IgG4Pro a single amino acid substitution
  • IgG4Pro may be introduced to abolish the heterogeneity observed in recombinant IgG4 antibody (see, e.g., Angal et al., Mol Immunol 30:105-108, 1993).
  • an “EC 50 ” as used herein in the context of a binding or functional assay refers to the half maximal effective concentration, which is the concentration of an antibody that induces a response (readouts can include but are not limited to fluorescence or luminescence signals) halfway between the baseline and maximum after a specified exposure time.
  • the “fold over EC 50 ” is determined by dividing the EC 50 of a reference antibody by the EC 50 of the test antibody.
  • K D Equilibrium dissociation constant
  • K D refers to the dissociation rate constant (k d , time -1 ) divided by the association rate constant (k a , time -1 M -1 ).
  • antibodies of the present disclosure have a K D of less than about 50 nM, typically less than about 25 nM, or less than 10 nM, e.g., less than about 5 nM or than about 1 nM and often less than about 10 nM as determined by surface plasmon resonance analysis using a biosensor system such as a Biacore ® system performed at 37°C.
  • an antibody of the present disclosure has a K D of less than 5 x 10 -5 M, less than 10- 5 M, less than 5 x 10 -6 M, less than 10 -6 M, less than 5 x 10 -7 M, less than 10 -7 M, less than 5 x 10 -8 M, less than 10 -8 M, less than 5 x 10 -9 M, less than 10 -9 M, less than 5 x10 -10 M, less than 10 -10 M, less than 5 x 10 -11 M, less than 10 -11 M, less than 5 x 10 -12 M, less than 10 -12 M, less than 5 x 10 -13 M, less than 10- 13 M, less than 5 x 10 -14 M, less than 10 -14 M, less than 5 x 10 -15 M, or less than 10 -15 M or lower as measured as a bivalent antibody.
  • an “improved” K D refers to a lower K D .
  • an antibody of the present disclosure has a K D of less than 5 x 10 -5 M, less than 10 -5 M, less than 5 x 10 -6 M, less than 10 -6 M, less than 5 x 10 -7 M, less than 10 -7 M, less than 5 x 10 -8 M, less than 10 -8 M, less than 5 x 10 -9 M, less than 10 -9 M, less than 5 x10 -10 M, less than 10 -10 M, less than 5 x 10 -11 M, less than 10 -11 M, less than 5 x 10 -12 M, less than 10 -12 M, less than 5 x 10 -13 M, less than 10 -13 M, less than 5 x 10 -14 M, less than 10 -14 M, less than 5 x 10 -15 M, or less than 10 -15 M or lower as measured as a monovalent antibody, such as a monovalent Fab.
  • an EphA2 antibody of the present disclosure has K D less than 100 pM, e.g., or less than 75 pM, e.g., in the range of 1 to 100 pM, when measured by surface plasmon resonance analysis using a biosensor system such as a Biacore ® system performed at 37°C.
  • an EphA2 antibody of the present disclosure has K D of greater than 100 pM, e.g., in the range of 100-1000 pM or 500-1000 pM when measured by surface plasmon resonance analysis using a biosensor system such as a Biacore ® system performed at 37°C.
  • EphA2 antibody is used interchangeably with “anti-EphA2 antibody” in this application.
  • the term “monovalent molecule” as used herein refers to a molecule with one antigen- binding site, e.g., a Fab or scFv.
  • the term “bivalent molecule” as used herein refers to a molecule with two antigen-binding sites.
  • a bivalent molecule of the present disclosure is a bivalent antibody or a bivalent fragment thereof.
  • a bivalent molecule of the present disclosure is a bivalent antibody.
  • a bivalent molecule of the present disclosure is an IgG.
  • monoclonal antibodies have a bivalent basic structure.
  • IgG and IgE have only one bivalent unit, while IgA and IgM consist of multiple bivalent units (2 and 5, respectively) and thus have higher valencies. This bivalency increases the avidity of antibodies for antigens.
  • the terms “monovalent binding” or “monovalently binds to” as used herein refer to the binding of one antigen-binding site to its antigen.
  • bivalent binding or “bivalently binds to” as used herein refer to the binding of both antigen-binding sites of a bivalent molecule to its antigen.
  • both antigen- binding sites of a bivalent molecule share the same antigen specificity.
  • valency refers to the number of different binding sites of an antibody for an antigen.
  • a monovalent antibody comprises one binding site for an antigen.
  • a bivalent antibody comprises two binding sites for the same antigen.
  • a multivalent antibody comprises two or more binding sites for the same antigen.
  • a trivalent antibody comprises three binding sites for the same antigen.
  • a tetravalent antibody comprises four binding sites for the same antigen.
  • the term “avidity” as used herein in the context of antibody binding to an antigen refers to the combined binding strength of multiple binding sites of the antibody.
  • bivalent avidity refers to the combined strength of two binding sites.
  • identity in the context of two or more polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same (e.g., at least 70%, at least 75%, at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher) identity over a specified region, e.g., the length of the two sequences, when compared and aligned for maximum correspondence over a comparison window or designated region.
  • Alignment for purposes of determining percent amino acid sequence identity can be performed in various methods, including those using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity the BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res.25:3389-3402 (1977) and Altschul et al., J. Mol. Biol.215:403-410 (1990). Thus, for purposes of this invention, BLAST 2.0 can be used with the default parameters to determine percent sequence identity.
  • a “conservative” substitution as used herein refers to a substitution of an amino acid such that charge, polarity, hydropathy (hydrophobic, neutral, or hydrophilic), and/or size of the side group chain is maintained.
  • Illustrative sets of amino acids that may be substituted for one another include (i) positively-charged amino acids Lys and Arg; and His at pH of about 6; (ii) negatively charged amino acids Glu and Asp; (iii) aromatic amino acids Phe, Tyr and Trp; (iv) nitrogen ring amino acids His and Trp; (v) aliphatic hydrophobic amino acids Ala, Val, Leu and Ile; (vi) hydrophobic sulfur-containing amino acids Met and Cys, which are not as hydrophobic as Val, Leu, and Ile; (vii) small polar uncharged amino acids Ser, Thr, Asp, and Asn (viii) small hydrophobic or neutral amino acids Gly, Ala, and Pro; (ix) amide-comprising amino acids Asn and Gln; and (xi) beta-branched amino acids Thr, Val, and Ile.
  • nucleic acid and “polynucleotide” are used interchangeably and as used herein refer to both sense and anti-sense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above.
  • a nucleotide refers to a ribonucleotide, deoxynucleotide or a modified form of either type of nucleotide, or combinations thereof.
  • the terms also include, but is not limited to, single- and double-stranded forms of DNA.
  • a polynucleotide e.g., a cDNA or mRNA
  • a polynucleotide may include either or both naturally occurring and modified nucleotides linked together by naturally occurring and/or non-naturally occurring nucleotide linkages.
  • the nucleic acid molecules may be modified chemically or biochemically or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art.
  • Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analogue, internucleotide modifications such as uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, and the like), charged linkages (e.g., phosphorothioates, phosphorodithioates, and the like), pendent moieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen, and the like), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, and the like).
  • uncharged linkages e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, and the like
  • charged linkages e.g., phosphorothioates, phosphorodithioates, and the like
  • a reference to a nucleic acid sequence encompasses its complement unless otherwise specified.
  • a reference to a nucleic acid molecule having a particular sequence should be understood to encompass its complementary strand, with its complementary sequence.
  • the term also includes codon-optimized nucleic acids that encode the same polypeptide sequence.
  • vector refers to a nucleic acid molecule capable of propagating another nucleic acid to which it is linked.
  • vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced.
  • a “vector” as used here refers to a recombinant construct in which a nucleic acid sequence of interest is inserted into the vector. Certain vectors can direct the expression of nucleic acids to which they are operatively linked. Such vectors are referred to herein as “expression vectors”. [0119]
  • substitution denotes the replacement of one or more amino acids or nucleotides by different amino acids or nucleotides, respectively.
  • An “isolated” nucleic acid refers to a nucleic acid molecule that has been separated from a component of its natural environment.
  • An isolated nucleic acid includes a nucleic acid molecule contained in cells that ordinarily contain the nucleic acid molecule, but the nucleic acid molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location.
  • isolated nucleic acid encoding an antibody or fragment thereof refers to one or more nucleic acid molecules encoding antibody heavy or light chains (or fragments thereof), including such nucleic acid molecule(s) in a single vector or separate vectors, and such nucleic acid molecule(s) present at one or more locations in a host cell.
  • the terms “host cell,” “host cell line,” and “host cell culture” are used interchangeably and refer to cells into which exogenous nucleic acid has been introduced, including the progeny of such cells.
  • a host cell can be a recombinant host cell, a primary transformed cell and progeny derived therefrom without regard to the number of passages.
  • a polypeptide “variant,” as the term is used herein, is a polypeptide that typically differs from one or more polypeptide sequences specifically disclosed herein in one or more substitutions, deletions, additions and/or insertions.
  • cancer cell or “tumor cell” as used herein refers to a neoplastic cell. The term includes cells from tumors that are benign as well as malignant. Neoplastic transformation is associated with phenotypic changes of the tumor cell relative to the cell type from which it is derived.
  • the changes can include loss of contact inhibition, morphological changes, and unregulated cell growth,
  • therapeutic agent refers to an agent that will cure, or at least partially arrest the symptoms of a disease and complications associated with the disease when administered to a patient suffering from the disease in a therapeutically effective dose.
  • a tumor overexpressing EphA2 refers to a tumor or cancer that expresses EphA2 or demonstrates EpA2 reactivity at a level that higher than the level of EphA2 expressed or EphA2 reactivity in normal tissue (e.g., tumor adjacent tissues or TAT).
  • a tumor or cancer that overexpresses EphA2 is one that expresses EphA2 at a level that is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 80%, or at 100% higher than the normal tissue (e.g., tumor adjacent tissues or TAT).
  • a tumor or cancer that overexpresses EphA2 is one that demonstrates EphA2 reactivity at level that is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 80%, or at 100% higher than the normal tissue (e.g., tumor adjacent tissues or TAT).
  • the disclosure additionally provides methods of identifying subjects who are candidates for treatment with an EphA2 antibody having tumor-targeting effects.
  • the invention provides a method of identifying a patient who can benefit from treatment with an EphA2 antibody of the present disclosure.
  • the patient has tumor that expresses EphA2.
  • the patient has tumor that overexpresses EphA2.
  • the tumor sample is from a primary tumor.
  • the tumor sample is a metastatic lesion. Binding of antibody to tumor cells through a binding interaction with the EphA2 can be measured using any assay, such as immunohistochemistry or flow cytometry.
  • binding of antibody to at least 0.2%, 0.5%, or 1%, or at least 5% or 10%, or at least 20%, 30%, or 50%, of the tumor cells in a sample may be used as a selection criterion for determining a patient to be treated with an EphA2 antibody as described herein.
  • analysis of components of the blood e.g., circulating protein levels, is used to identify a patient whose tumor cells are overexpressing EphA2.
  • An EphA2 antibody disclosed herein can be used to treat several different cancers.
  • a cancer patient who can benefit from the treatment of the EphA2 antibody has a cancer expressing EphA2.
  • a cancer patient who can benefit from the treatment of the EphA2 antibody has a cancer overexpressing EphA2.
  • the cancer is a carcinoma or a sarcoma.
  • the term “an antibody binds to an EphA2” or “an antibody binds to EphA2,” means that the antibody binds to EphA2 under permissible conditions (e.g., in a suitable buffer), and the detected signal resulted from the binding is at least 2-fold, at least 5-fold, at least 10 fold, at least 20 fold, at least 100 fold, at least 150 fold, or at least 200 fold above a reference level.
  • the reference level is a detected signal produced by contacting a control antibody with the EphA2, or by contacting the antibody with a control protein.
  • sibling antibodies refer to antibodies derived from the same B-cell clonal lineage. In some embodiments, sibling antibodies share sequence and structural properties as well as epitope specificity.
  • the term “convergent antibodies” refer to that antibodies derived from different B-cell lineages that exhibit similar sequence and structural properties.
  • Several anti-EphA2 comparator antibodies are referenced in this disclosure.
  • AB-010018 is a mouse monoclonal antibody precursor of clinical candidate humanized DS-8895a (Daiichi Sankyo Company, Ltd.), as disclosed in US9150657, SEQ ID NO: 35 and 37, Hasegawa J. et al., Cancer Biol Ther.2016 Nov;17(11):1158-1167. doi: 10.1080/15384047.2016.1235663. Epub 2016 Sep 21; Shitara K. et al., J Immunother Cancer, 2019 Aug 14;7(1):219.
  • AB-010016 is an anti-EphA2 antibody generated based on clinical candidate Medi-547 (MedImmune, Inc.) It was generated using the V H and V L amino acid sequences from Protein Data Bank code 3SKJ, Peng, L., et.al, (2011) J Mol Biol 413: 390-405.
  • AB-010017 is an anti-EphA2 antibody generated based on clinical candidate MM-310 (Merrimack, Inc.) It was generated using V H and V L amino acid sequences from the scFv of SEQ ID NO: 40 in US20190070113A1; See also, Geddie et al., MAbs.
  • This application relates to tumor-targeting antibodies that bind to EphA2 and bind preferentially to tumor tissues than normal tissues.
  • the EphA2 antibody binds to one or more epitopes in the FN2 domain of EphA2.
  • the EphA2 antibodies disclosed herein can target a tumor in a variety of ways, for example, it can mediate antibody-dependent cell-mediated cytotoxicity (ADCC) and/or ADCP to target and kill tumor cells.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • EphA2 antibodies demonstrate significant cytotoxicity towards tumor cells and show therapeutic potential in treating cancers.
  • Some of the EphA2 antibodies can target both mouse tumor and human tumor cells.
  • the EphA2 antibodies are also useful in detecting tumors suitable for treatment in diagnostic applications.
  • EphA2 antibodies provided in this disclosure showed a higher binding affinity to various tumors and lower binding to normal tissues (e.g., tumor adjacent tissues) and exhibit differential binding profile on various cancer tumor types.
  • normal tissues e.g., tumor adjacent tissues
  • the EphA2 antibodies disclosed herein exhibit reduced agonistic or antagonistic effects on the EphA2 receptor. These properties render them ideal for use as cancer therapeutics.
  • Ephrin receptor A2 (EphA2) is expressed mainly in proliferating epithelial cells in adults. Under normal conditions, EphA2 interacts with membrane proteins, ephrin A1, on the neighboring cell and induce diverse signaling networks following cell-to-cell contact. For example, EphA2 may decrease in cell-extracellular matrix (ECM) attachment upon phosphorylation.
  • EphA2 is overexpressed in many solid tumors including melanoma, glioma, prostate cancer, breast cancer, ovarian cancer, lung cancer, colon cancer, esophageal cancer, gastric cancer cervical cancer, bladder cancer.
  • EphA2 contributes to cell adhesion and angiogenesis, and its expression is also linked to increased malignancy and poor prognosis.
  • Human EphA2 has a sequence of [0138] EPHA2 comprises an ectodomain, an intracellular region, and a single transmembrane helix.
  • the ectodomain of EphA2, consisting of amino acid residues 23-546 using SEQ ID NO: 94 as a reference, comprises a ligand binding domain (LBD), which interacts with ephrin A1, a Sushi domain, an epidermal growth factor like domain, and two fibronectin type III domains (FN1 and FN2).
  • LBD ligand binding domain
  • the intracellular region comprises a tyrosine kinase domain and a sterile ⁇ -motif domain.
  • the transmembrane helix of the protein is flanked by juxtamembrane linkers, which connects the ectodomain and the intracellular domain.
  • a membrane-binding motif FN2 located within amino acid residues 437-534 of SEQ ID NO: 94, includes positively charged residues, which can recruit negatively charged lipids to the site of membrane-protein interaction.
  • the interactions of FN2 with lipids stabilize the otherwise flexible EphA2 ectodomain in two main conformations relative to the membrane. [0139]
  • the EphA2 ectodomain is highly conserved across species.
  • EphA2 has sequence identity of 90.8%, 90.4%, 98.8%, and 98.8% to mouse, rat, macaque, and cyno, respectively.
  • EPHA2 ANTIBODIES [0140]
  • an EphA2 antibody may be any one of AB-008873, the siblings and variants thereof, as further described below.
  • AB-008873 was discovered in antibody repertoires generated by Immune Repertoire Capture ® (IRCTM) technology from plasmablast B cells isolated from a non-small cell lung cancer patient with an active anti-tumor immune response after treatment with the anti-PD-1 antibody OPDIVO® (nivolumab) (Bristol Myers Squibb).
  • IRCTM Immune Repertoire Capture ®
  • OPDIVO® nivolumab
  • WO 2012148497A2 the entire content of which is herein incorporated by reference.
  • AB-008873 aligns to its closest human germline genes (IGHV4-34*02, IGHD2-8*01, IGHJ3*02, IGLV3-21*02, and IGLJ2*01), and to its four known siblings AB-009805, AB-009806, AB-009807, and AB-009808. Structures of these antibodies are further disclosed below, e.g., in Tables 6-8. Variants [0142] In some embodiments, variants of any of the EphA2 antibodies disclosed herein can be generated by introducing mutations to the heavy chain and/or light chain sequences.
  • the mutation(s) are introduced into one or more of the CDRs of an EphA2 antibody disclosed herein, e.g., AB-008873, AB-010148, or AB-010363. In some embodiments, the mutation(s) are introduced in the framework regions.
  • an EphA2 antibody provided herein comprises a V H region of any one of SEQ ID NO 67-77 and 591-655, and/or a V L region of any one of SEQ ID NO: 78-88 and 656-720, or an antibody comprising a V H region with at least 80% identity to any one of SEQ ID NO 67-77 and 591-655 and a V L region having at least 80% identity to any one of SEQ ID NO: 78-88 and 656-720, with variations to the corresponding V H or V L regions present only in Framework regions.
  • EphA2 antibody provided herein comprises an HCDR1 of any one of SEQ ID NOS:1-11, and 201-265, an HCDR2 of any one of SEQ ID NOS:12-22 and 266-330, an HCDR3 of any one of SEQ ID NOS:23-33 and 331-395, an LCDR1 of any one of SEQ ID NOS:34-44 and 396-460, an LCDR2 of any one of SEQ ID NOS:45-55 and 461-525, an LCDR3 of any one of SEQ ID NOS:56-66 and 526-590; and the FW regions in the V H region are at least 80% identical to the FW regions present in the V H region of SEQ ID NO 67-77 and 591-655, and wherein the FW regions in the V L region are at least 80% identical to the FW regions present in the V L region of SEQ ID NO: 78-88 and 656-720 [0144] In some embodiments, a variant is engineered to
  • a variant e.g., AB-009812
  • a variant comprises a mutation H54RS relative to AB-008873 (heavy chain position 54 mutated from arginine to serine).
  • a variant e.g., AB-009813
  • a mutation H54RA relative to AB-008873 (heavy chain position 54 mutated from arginine to alanine).
  • a variant (e.g., AB- 009814) comprises deletion of three residues, H61N-H62Y-H63N, relative to AB-008873.
  • a variant comprises one or more mutations selected from the group consisting of H54RS, H54RA, and deletions of three residues H61N-H62Y-H63N, relative to the sequence of the heavy chain variable region of AB-008873 (SEQ ID NO: 67).
  • Variant antibodies AB-009812, AB-009813, and AB- 009814 are described in Tables 1-3. [0145] Additional variants antibodies may also be generated by introducing one or more mutations to any one of the AB-008873 and its siblings.
  • a variant comprises one or more mutations selected from the group consisting of H31DG, L31NS, L97LV, H51VI, H86TS, H129AS, and L60QR relative to AB-009815.
  • H V and L V sequences of the AB-009815 SEQ ID NO: 75 and 86 as references.
  • the name indicates whether the mutation is a heavy chain or light chain, the position in the heavy chain or light chain of the mutation, the amino acid residue at the position before introduction of the mutation, and the amino acid at the position after introduction of the mutation.
  • H129AS refers to that the alanine at heavy chain position 129 is mutated to a serine.
  • Table 1 shows exemplary variants of AB-009815. Table 1.
  • Exemplary variants of AB-009815 Further mutations can be introduced to any one of the AB-008873 variants listed in Table 1. For example, one or more mutations are introduced to AB-0010148 and exemplary variants resulted from the further mutagenesis are shown in in Table 2, below.
  • Table 2 Exemplary AB-0010148 variants [0147] Further mutations can be introduced to any one of the AB-0010148 variants listed in Table 2. For example, one or more mutations are introduced to AB-010357, AB-010361, AB-010363, and exemplary antibodies resulted from the further mutagenesis are shown in in Table 3, 4, 5, respectively.
  • Table 3 Exemplary variants of AB-010357 Table 4.
  • Exemplary variants of AB-010361 Table 5 shows exemplary variants of AB-010363 [0148] Methods of generating variants are further described in the section entitled “ENGINEERING VARIANTS” and Example 2 below.
  • an EphA2 antibody that binds to EphA2 and comprises a heavy chain variable region comprising: an HCDR1 comprising a sequence (SEQ ID NO:1), or a variant HCDR1 in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence; an HCDR2 comprising a sequence (SEQ ID NO:12), or a variant HCDR2 in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence; and an HCDR3 comprising a sequence (SEQ ID NO:23), or a variant HCDR3 in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence.
  • the antibody comprises a light chain variable region comprising: an LCDR1 comprising a sequence (SEQ ID NO:34), or a variant LCDR1 in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence; an LCDR2 comprising a sequence (SEQ ID NO:45), or variant LCDR2 in which 1, 2, or 3 amino acid is substituted relative to the sequence; and an LCDR3 comprising a sequence (SEQ ID NO:56), or a variant LCDR3 in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence.
  • an antibody that binds to EphA2 comprises: a heavy chain variable region comprising: an HCDR1 of any one of SEQ ID NOS: 1-11 and 201-265 or a variant thereof in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence; an HCDR2 of any one of SEQ ID NOS: 12-22 and 266-330 or a variant thereof in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence; and an HCDR3 of any one of SEQ ID NOS: 23-33 and 331-395 or a variant thereof in which 1, 2, 3, 4, or 5 amino acids are substituted relative to the sequence.
  • the antibody also comprises a light chain variable region comprising: an LCDR1 of any one of SEQ ID NOS: 34-44 and 396-460 or a variant thereof in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence; an LCDR2 of any one of SEQ ID NOS: 45-55 and 461-525 or a variant thereof in which 1, 2, or 3 amino acid is substituted relative to the sequence; and an LCDR3 of any one of SEQ ID NOS: 56-66 and 526- 590 or a variant thereof in which 1, 2, 3, 4, or 5 amino acid is substituted relative to the sequence.
  • an antibody that binds to EphA2 comprises (a) an HCDR1 sequence of GGSX 1 X 2 X 3 YX 4 WS where X 1 is F or L, X 2 is S or N, and X 3 is D or G, and X 4 is Y or H (SEQ ID NO: 769); (b) an HCDR2 sequence of EX 1 NHX 2 GSX 3 X 4 YNNYNPSLKS, where X 1 is I or V, X 2 is A, Q, R or S, X 3 is I or T, and X 4 is N or S (SEQ ID NO: 770); and (c) an HCDR3 sequence of AKPX 1 RPHC X 2 NGVCX 3 SGDAFDI, where X 1 is L or F, X 2 is I or T; and X 3 is Y or S(SEQ ID NO: 771).
  • the antibody also comprises (d) an LCDR1 sequence of X 1 GNNIGX 2 X 3 X 4 VH, where X 1 is G or R, X 2 is S, T, or Y, X 3 is K or M, and X 4 is N or S (SEQ ID NO: 772); I an LCDR2 sequence of DDSDRPS (SEQ ID NO: 45); and (f) an LCDR3 sequence of QVWDX1 X2SDHX3V, where X1 is H or S, X2 is E, R, or S, and X3 is L or V (SEQ ID NO: 773).
  • an antibody that binds to EphA2 comprises (a) an HCDR1 sequence of GGSX1X2 X3YX4WS where X1 is F or L, X2 is S or N, and X3 is D or G, and X4 is Y or H (SEQ ID NO: 769); (b) an HCDR2 sequence of EX 1 NHX 2 GSX 3 X 4 YNPSLKS, where X 1 is I or V, X 2 is A, Q, R or S, X 3 is I or T, and X 4 is N or S (SEQ ID NO: 774); or an HCDR2 sequence of EX 1 NHX 2 GS X 3 X 4 YNNYNPSLKS, where X 1 is I or V, X 2 is R or S, X 3 is I or T, and X 4 N or S (SEQ ID NO: 777); and (c) an HCDR3 sequence of AKPX 1 RPHC
  • the antibody also comprises (d) an LCDR1 sequence of X 1 GNNIGX 2 X 3 X 4 VH, where X 1 is G or R, X 2 is S, T, or Y, X 3 is K or M, and X 4 is N or I (SEQ ID NO: 780) (e) an LCDR2 sequence of DDSDRPS (SEQ ID NO: 45); and (f) an LCDR3 sequence of QVWDX1 X2SDHX3V, where X1 is H or S, X2 is E, R, or S, and X3 is L or V. (SEQ ID NO: 773).
  • an antibody that binds to EphA2 comprises a V H comprising an amino acid sequence having at least 95% identity to (SEQ ID NO: 67); and a V L comprising an amino sequence having at 95% identity to (SEQ ID NO: 78).
  • an antibody that binds to EphA2 has a V H comprising an amino acid sequence having at least 95% identity to any one of SEQ ID NO: 67-77 and 591-655; and a V L comprising an amino sequence having at 95% identity to any one of SEQ ID NOs: 78-88 and 656-720.
  • an antibody that binds to EphA2 comprises a heavy chain variable (V H ) region and a light chain variable (V L ) region.
  • the V H region has at least 70% amino acid sequence identity to SEQ ID NO:67; and comprises a CDR1 of SEQ ID NO:1, or the CDR1 of SEQ ID NO:1 in which 1, 2, 3, 4, or 5 amino acids are substituted; a CDR2 of SEQ ID NO:83, or the CDR2 of SEQ ID NO:12 in which 1, 2, 3, 4, or 5 amino acids are substituted; a CDR3 of SEQ ID NO:23 or the CDR3 of SEQ ID NO:23 in which 1, 2, 3, 4, or 5 are substituted.
  • the V L region has at least 70% amino acid sequence identity to SEQ ID NO: 78, and comprises a CDR1 of SEQ ID NO:34 or the CDR1 of SEQ ID NO:34 in which 1, 2, 3, 4, or 5 amino acids are substituted; a CDR2 of SEQ ID NO:45, or the CDR2 of SEQ ID NO:45 in which 1, 2, 3, 4, or 5 amino acids are substituted; a CDR3 of SEQ ID NO:56 or the CDR3 of SEQ ID NO:56 in which 1, 2, 3, 4, or 5 are substituted.
  • an antibody that binds to EphA2 comprises: a V H region comprising amino acid sequence SEQ ID NO:67 and a V L region comprising amino acid sequence SEQ ID NO:78; a V H region comprising amino acid sequence SEQ ID NO:68 and a V L region comprising amino acid sequence SEQ ID NO:79; a V H region comprising amino acid sequence SEQ ID NO:69 and a V L region comprising amino acid sequence SEQ ID NO:80; a V H region comprising amino acid sequence SEQ ID NO:70 and a V L region comprising amino acid sequence SEQ ID NO:81; a V H region comprising amino acid sequence SEQ ID NO:71 and a V L region comprising amino acid sequence SEQ ID NO:82; a V H region comprising amino acid sequence SEQ ID NO:72 and a V L region comprising amino acid sequence SEQ ID NO:83; a V H region comprising amino acid sequence SEQ ID NO:73 and a V L region comprising amino acid sequence SEQ
  • an EphA2 antibody of the present disclosure has one, two, or three CDRs of a V L sequence in Table 7.
  • the EphA2 antibody has at least one mutation and no more than 10, 20, 30, 40 or 50 mutations in the V L amino acid sequences compared to a V L sequence set forth in Table 8.
  • the V L amino acid sequence may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid insertions or deletions compared to a V L sequence set forth in Table 8.
  • the V L amino acid sequence may comprise a deletion or insertion, e.g., a 1, 2, 3, 4, 5, 6, or 7 amino acid deletion or insertion, relative to a CDR sequence shown in Table 7.
  • the V L region comprises a CDR1 having 1 or 2 substitutions in relative to a CDR1 sequence shown in Table 7. In some embodiments, a CDR1 has 3, 4, or 5 substitutions relative to a CDR1 sequence shown in Table 7. In some embodiments, the V L region comprises a CDR2 with 1 or 2; or 1, 2, or 3; substitutions relative to the CDR2 sequence shown in Table 7. In some embodiments, the V L region comprises a CDR3 with 1, 2, or 3; or 1, 2, 3, or 4; substitutions relative to a CDR3 sequence shown in Table 7.
  • an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3, each having at least 70% identity to a CDR1, CDR2, and CDR3 as shown in Table 7. In some embodiments, an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3, each having at least 80% identity to a CDR1, CDR2, and CDR3 as shown in Table 7. In some embodiments, an anti-tumor antibody of the present disclosure comprises a CDR1, CDR2, and CDR3 as shown in Table 7.
  • an EphA2 antibody of the present disclosure comprises HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 of an antibody designated as AB-008873; AB-009805; AB-009806; AB-009807; AB-009808; AB-009812; AB- 009813; AB-009814; AB-009815; AB-009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB-010147, AB-010148, AB-010149, AB-010150, AB- 010151, AB-010152, AB-010357, AB-010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB-010364, AB-010365, AB-010366,
  • an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3 of the VL of an antibody designated as AB-010361 or AB-010699.
  • AB-008873; AB-009805; AB-009806; AB-009807; AB-009808 are sibling antibodies as they are derived from the same lineage as AB-008873. See Example 1.
  • the antibody comprises a heavy chain variable region and a light chain variable region of an antibody designated as AB-008873; AB-009805; AB-009806; AB-009807; AB- 009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB-010147, AB-010148, AB- 010149, AB-010150, AB-010151, AB-010152, AB-010357, AB-010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB-010364, AB-010365, AB-010366, AB-010367, AB- 010661,
  • an EphA2 antibody of the present disclosure has one, two, or three CDRs of a V H sequence in Table 8.
  • the EphA2 antibody has at least one mutation and no more than 10, 20, 30, 40 or 50 mutations in the VH amino acid sequences compared to a VH sequence set forth in Table 8.
  • the V H amino acid sequence may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid insertions or deletions compared to a V H sequence set forth in Table 8.
  • the V H amino acid sequence may comprise a deletion or insertion, e.g., a 1, 2, 3, 4, 5, 6, or 7 amino acid deletion or insertion, relative to a CDR sequence shown in Table 6.
  • the V H region comprises a CDR1 having 1 or 2 substitutions in relative to a CDR1 sequence shown in Table 6. In some embodiments, a CDR1 has 3, 4, or 5 substitutions relative to a CDR1 sequence shown in Table 6. In some embodiments, the V H region comprises a CDR2 with 1 or 2; or 1, 2, or 3; substitutions relative to the CDR2 sequence shown in Table 6. In some embodiments, the V H region comprises a CDR3 with 1, 2, or 3; or 1, 2, 3, or 4; substitutions relative to a CDR3 sequence shown in Table 6.
  • an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3, each having at least 70% identity to a CDR1, CDR2, and CDR3 as shown in Table 6. In some embodiments, an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3, each having at least 80% identity to a CDR1, CDR2, and CDR3 as shown in Table 6. In some embodiments, an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3 as shown in Table 6.
  • an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3 of an antibody designated as AB-008873; AB-009805; AB-009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB- 009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB-010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB- 010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB-010364, AB-010365, AB-010366, AB-010367, AB-010661
  • an EphA2 antibody of the present disclosure comprises a CDR1, CDR2, and CDR3 of the VH of an antibody designated as AB-010361 and AB-010699.
  • Exemplary EphA2 antibodies include AB-008873; AB-009805; AB-009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; AB-009817, AB- 010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB-010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB-010358, AB-010359, AB- 010360, AB-010361, AB-010362, AB-010363,
  • the EphA2 antibody is AB-010361 or AB-010699.
  • These exemplary EphA2 antibodies have structures (HCDRs, LCDRs, V H and/or V L sequences) shown in Tables 6-8. Table 6. Heavy chain CDRs
  • the EphA2 antibody disclosed herein comprises a heavy chain variable region and a light chain variable region of an antibody designated as AB-008873; AB-009805; AB- 009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB- 010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB-010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB-010364, AB-010365, AB- 010366, AB-010367,
  • the variant comprises a heavy chain variable region having a sequence that is at least 95% identical to that of the corresponding heavy chain variable region and a light chain variable region having a sequence that is at least 95% identical to the corresponding light chain variable region.
  • the variant may comprise a V H that is at least 95% identical to that of AB-008873, AB-010148, AB- 010363, or AB-010699 and/or a V L that is at least 95% identical to that of AB-008873, AB-010148, AB-010363, or AB-010699.
  • the EphA2 antibody disclosed herein comprises a heavy chain variable region and a light chain variable region of an antibody designated as AB-010361 or AB-010699.
  • the EphA2 antibody disclosed herein comprises an HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 of an antibody designated as AB-008873; AB-009805; AB- 009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB- 010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB
  • the EphA2 antibody disclosed herein comprises an HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3 of an antibody designated as AB-010361 or AB-010699.
  • An EphA2 antibody disclosed herein binds to an epitope in the EphA2 protein (SEQ ID NO: 94).
  • an EphA2 antibody disclosed herein binds to an epitope in the FN2 domain of the EphA2 protein.
  • the binding can be detected using yeast display experiments illustrated in FIG.6.
  • the FN2 domain consists of residues 437-534 of SEQ ID NO: 94 and has a sequence of SEQ ID NO: 95 (TEPPKVRLEGRSTTSLSVSWSIPPPQQSRVWKYEVTYRKKGDSNSYNVRRTEGFSVTLDDLA PDTTYLVQVQALTQEGQGAGSKVHEFQTLSPEGSGN).
  • the epitope recognized by an EphA2 antibody disclosed herein overlaps with that of AB-010018.
  • Epitopes for the EphA2 antibodies disclosed herein can be determined by any method well known in the art, for example, by conventional immunoassays.
  • the epitope to which the EphA2 antibody binds can be determined in a systematic screening by using overlapping peptides derived from the EphA2 sequence and determining binding by the antibody.
  • the generation and characterization of antibodies may elucidate information about desirable epitopes. This information may allow screening for antibodies that compete for binding to the same epitope, e.g., an epitope in the FN2 domain of the EphA2 protein.
  • an epitope binning method is performed, e.g., using Bio-layer interferometry (BLI) as described in Example 4.
  • the underlying principle of epitope binning is that proteins with overlapping binding sites will sterically inhibit simultaneous binding.
  • the antigen is pre-saturated with t he 1st monoclonal antibody (mAb)
  • the 2 nd mAb is applied and signal from the binding of the 2 nd mAb to the antigen is detected and quantified.
  • a significantly reduced signal from binding of 2 nd mAb to the antigen indicates that there are overlapping binding sites between the two antibodies. Pair-wise interactions of the antibodies are scored and used to bin the antibodies into sets defined by mutual competition.
  • Epitope binning is useful for antibody characterization because antibodies in a bin may exhibit similar MOAs. Binning with antibodies with antibodies of known reactivity can inform epitope identification.
  • An EphA2 antibody disclosed herein binds to at least one, at least two, at least three, at least four, at least five residues selected from the group consisting of Pro439, Lys441, Arg443, Leu444, Arg447, Lys476, Gly477, Leu504, Gln506, Ser519, Lys520, Val521, His522, Glu523, Phe524, and Gln525, with the residue numbering referring to the EphA2 amino acid sequence of SEQ ID NO: 94.
  • the EphA2 antibody binds to at least one, at least two, at least three, at least four, at least five residues, at least six residues, at least seven residues, at least eight residues, or at least nine residues selected from the group consisting of Leu444, Arg447, Lys476, Gln506, Ser519, Lys520, Val521, Glu523, Phe524, and Gln525. In one embodiment, the EphA2 antibody binds to all the residues Leu444, Arg447, Lys476, Gln506, Ser519, Lys520, Val521, Glu523, Phe524, and Gln525.
  • the EphA2 antibody bind to a conformational epitope that is in one, two, three and/or four regions in the EphA2 protein: a first region consisting of amino acid residues 439-447, a second region consisting of amino acid residues 476-477, a third region consisting of amino acid residues 504-506, and a fourth region consisting of amino acid residues 519-525.
  • the epitope that the EphA2 antibody binds is conserved across species of cyno, rat, mouse and human, all of which are commonly used in toxicology studies.
  • FIG.46, FIG.44 and 45 Seiradake et al., Nat. Struct. Mol.
  • EphA2 antibodies as described herein can be assessed for binding in binding assays.
  • suitable assays include surface plasmon resonance analysis using a biosensor system such as a Biacore ® system or a flow cytometry assay, which are further described in the EXAMPLES section.
  • binding to EphA2 protein is assessed in a competitive assay format with a reference antibody AB-008873 or a reference antibody having the variable regions of AB- 008873.
  • a variant EphA2 antibody in accordance with the present disclosure may block binding of the reference antibody in a competition assay by about 50% or more.
  • binding assays to assess variant activity are performed on tumor tissues or tumor cells ex vivo, e.g., on tumor cells that were grown as a tumor graft in a syngeneic (immune-matched) mouse in vivo then harvested and processed within 24-48 hrs. Binding can be assessed by any number of means including flow cytometry.
  • the antibodies disclosed herein bind specifically to tumor cells. In some embodiments the antibody is added to a cancer cell line and the binding is analyzed using a flow cytometry.
  • AB-008873 showed a strong binding to 786-O, A375, A549, H522, LoVo, MDA-MB-231, PC3, RKO, SKOV3, SW1116, and CT26. Additionally, AB-008873 is also capable of binding to CT26 ex vivo cells.
  • FIG. 1 Tables 23 and 24. Its sibling antibodies AB-009805, AB-009806, AB-009807, and AB-009808 also showed binding activity to A549 cells, but less than that of AB-008873.
  • FIG.20 Unlike AB-010018 (mouse monoclonal antibody precursor of humanized DS-8895a.
  • AB-008873 demonstrated binding and ADCC activity on both A549 cells and CT26 cells.
  • FIG.4. the binding of the antibodies to bind to tumor cells are assessed by immunofluorescence methods, as described in the EXAMPLES. AB-008873 and its variants preferentially bind to various tumors but not to normal human tissues (FIGs.27-34).
  • AB-008873 advantageously showed less staining in normal tissues and a higher staining in tumor tissues.
  • the AB-008873 showed preferential binding to ovarian cancer and soft tissue sarcoma (STS) than the respective tumor adjacent tissue (TATs); in contrast, all commercial anti-EphA2 antibodies tested, exception for LS-C 36249-100, did not show any detectable binding in these two tumors (FIG. 27).
  • an EphA2 antibody disclosed herein demonstrate tumor selectivity (i.e., preferentially bind to tumor tissue than TATs) in different donors. That is to say, the antibody shows tumor selectivity in some donors but not other donors.
  • AB-008873 and its variant antibodies, AB-009812, AB-009813, AB-009815, and AB-009816 showed tumor selectivity in different donors in uterine cancer, head and neck cancer, and NSCLS (FIG. 28-30).
  • the antibody’s binding activity of functional activity is assessed by determining EC 50 values, and in some embodiments additionally determining delta activity, i.e., the difference in specific activity between lower and upper plateaus of the activation curve expressed as percent of activity of a selected antibody having known in vitro activity. In typical embodiments, EC 50 values are compared to a reference antibody.
  • an antibody comprising the VH and VL regions of an EphA2 antibody disclosed herein and a mouse IgG2a Fc region when testing binding or functional activity using a tumor cell line, is employed as a reference antibody and included in an assay to assess variant activity relative to the reference antibody.
  • an EphA2 antibody of the present disclosure exhibits no measurable agonistic effect on the ephrinA1-EphA2 signaling axis. In some embodiments, an EphA2 antibody of the present disclosure exhibits less agonistic effect on the ephrinA1-EphA2 signaling axis than the ephrin-A1 ligand.
  • an EphA2 antibody of the present disclosure activates the ephrin A1-EphA2 signaling axis at least 99%, 98% 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, or 50% less than ephrin-A1 activates the ephrin A1-EphA2 signaling axis.
  • an EphA2 antibody of the present disclosure activates the ephrin A1-EphA2 signaling axis at least 99%, 98%, 95%, 90%, 85%, or 80% less than ephrin-A1 activates the ephrin A1-EphA2 signaling axis.
  • an EphA2 antibody of the present disclosure shows weak agonistic effect on the ephrinA1-EphA2 signaling axis, with the effect occurring at a potency less than the potency of the ADCC of the antibody.
  • an EphA2 antibody of the present disclosure has an EC 50 for activation of the ephrinA1-EphA2 signaling axis that is at least 10-, 20-, 50-, 100-, 200-, 500-fold less potent than the ADCC EC 50 of the antibody.
  • an EphA2 antibody of the present disclosure exhibits no antagonistic effect on the ephrinA1-EphA2 signaling axis.
  • an EphA2 antibody of the present disclosure exhibits less antagonistic effect on the ephrinA1-EphA2 signaling axis than AB-010018.
  • FIG. 43B The first EphA2 antibody of the present disclosure exhibits less antagonistic effect on the ephrinA1-EphA2 signaling axis than AB-010018.
  • Methods for measuring ephrinA1-EphA2 signaling axis and the effect of the EphA2 antibodies described herein are well known. In some embodiments, it can be accomplished by detecting the phosphorylation of EphA2 protein for example, one or more of the residues Y588, Y772, S897 of the EphaA2 protein. The degree of phosphorylation can be quantified using methods well known in the art, for example, Western Blot analysis using antibodies specific to described phosphorylation sites.
  • One exemplary method of measuring ephrinA1-EphA2 signaling axis is disclosed in Example 5.
  • EphaA2 signaling provides a therapeutic advantage over other EphA2 antibodies that act as agonists or antagonists of the ephrin A1-EphA2 signaling axis by increasing the therapeutic index.
  • an EphaA2 antibody, or an immunoconjugate or bispecific version thereof, with limited effect on EphA2 signaling may be dosed at a level that provides both efficacy and safety while an EphaA2 antibody, or an immunoconjugate or bispecific version thereof, that agonizes the ephrin A1-EphA2 signaling axis could show a smaller, and potentially non-viable, therapeutic index.
  • an EphA2 antibody of the present disclosure comprises an Fc region with effector function.
  • effector functions include, but are not limited to, C1q binding and complement-dependent cytotoxicity (CDC), Fc receptor binding (e.g., Fc ⁇ R binding), ADCC, antibody- dependent cell-mediated phagocytosis (ADCP), down-regulation of cell surface receptors (e.g., B cell receptor), and B-cell activation. Effector functions may vary with the antibody class.
  • native human IgG1 and IgG3 antibodies can elicit ADCC and CDC activities upon binding to an appropriate Fc receptor present on an immune system cell; and native human IgG1, IgG2, IgG3, and IgG4 can elicit ADCP functions upon binding to the appropriate Fc receptor present on an immune cell.
  • the Fc region of the EphA2 antibodies disclosed herein may be an Fc region engineered to alter one or more functional properties of the antibody, such as serum half-life, complement fixation, Fc receptor binding, and/or ADCC. Accordingly, an Fc region can comprise additional mutations to increase or decrease effector functions, i.e., the ability to induce certain biological functions upon binding to an Fc receptor expressed on an immune cell.
  • Immune cells include, but are not limited to, monocytes, macrophages, neutrophils, dendritic cells, eosinophils, mast cells, platelets, B cells, large granular lymphocytes, Langerhans’ cells, natural killer (NK) cells, and cytotoxic T cells.
  • an antibody of the present disclosure has enhanced ADCC and/or serum stability compared to antibody AB-008873 when the antibodies are assayed in a human IgG1 isotype format.
  • the EphA2 antibodies of the present disclosure may be evaluated in various assays for their ability to mediate FcR-dependent activity. In one assay, the binding activity of an EphA2 antibody is evaluated in an Fc receptor engagement assay.
  • “engagement” of an Fc receptor occurs when a variant antibody binds to both a target tumor cell via its Fv region and an Fc ⁇ R present on an immune cell via the antibody Fc region in such as manner to transduce a signal. If the Fc region is kept constant among variants that differ in their Fv regions, then the assay allows an evaluation of tumor binding activity across such variants in the context of potential signal transduction through a particular Fc region binding a particular Fc receptor. In some embodiments, binding of the antibody Fc region can result in clustering and/or internalization of the FcR, resulting in a luminescence signal in cells harboring a NFAT-RE-Luciferase reporter construct.
  • an EphA2 antibody of the present disclosure has ADCC when the antibodies are assayed in a mouse IgG2a isotype format. In some embodiments, an EphA2 antibody of the present disclosure has ADCC activity that is comparable to that of AB-008873.
  • AB-008873 showed dose dependent ADCC on A549, MDA-MB- 231, CT26, and to a small extent EMT6. See FIG. 2A-2B and Table 25.
  • ADCP activity of an EphA2 antibody is assessed using fluorescently labeled, in vitro cultured tumor cells and Raw264.7 murine macrophages.
  • opsonization of the tumor cell by the antibody leads to phagocytosis detected by flow cytometry.
  • Variations of this assay have been described and can include co-labeling of tumor and effector cells or assessment of phagocytosis through FcyRIIa engagement (e.g., Fc ⁇ RIIa-H ADCP Reporter Bioassay from Promega).
  • FcyRIIa engagement e.g., Fc ⁇ RIIa-H ADCP Reporter Bioassay from Promega.
  • the ADCP activity of an EphA2 antibody is evaluated using the method described above and in more detail in EXAMPLE 3.
  • AB-008873 showed strong ADCP activity on A549 cells.
  • FIG.2B and FIG.20 showed strong ADCP activity on A549 cells.
  • the sibling antibodies AB-009805, AB-009806, AB-009807, and AB-009808 also showed ADCP activity, but less than that of AB-008873.
  • AB-008873 showed strong ADCP activity on A549 cells.
  • the sibling antibodies AB-009805, AB-009806, AB-009807, and AB-009808 also showed ADCP activity, but less than that of AB-008873.
  • An EphA2 antibody is deemed to have ADC activity if, when the antibody is conjugated to a drug molecule (toxin) to form an antibody drug conjugate (ADC), said ADC can kill target cells.
  • the antibody is deemed to have ADC activity if the EC50 of the assay measuring the cell killing activity of the ADC is less than 1E-08.
  • the ADC activity of the EphA2 antibody is evaluated using a drug-conjugated secondary antibody.
  • the antibody-drug conjugate assay involves tumor target cells, primary antibodies of interest (the EphA2 antibody to be tested), and a secondary antibody that is conjugated to a drug molecule, where the secondary antibody recognizes the primary antibody.
  • primary antibody dilutions are incubated with target cells at room temperature for a first period (for example, 10-30 minutes).
  • the drug-conjugated secondary antibody is then added to the incubation mixture containing the target cells and the primary antibody.
  • the mixture is then incubated for second period before measuring the extent of target cell lysis.
  • the assay generates a 100% cell lysis value by adding cell lysis buffer directly to target cell sample, which are not treated by the primary or drug-conjugated second antibody, and cell killing data from samples treated the antibody mixtures as disclosed above can be normalized to the value of 100% cell lysis.
  • the results of the assay can be used to predict whether an ADC produced by conjugating a particular antibody and the drug molecule can kill target cells.
  • activity of an EphA2 antibody variant is evaluated in vivo in a suitable animal tumor model.
  • a reduction in tumor load reflects the anti-tumor function of an antibody.
  • a variant of an antibody as described herein has at least 50%, or at least 60%, or 70%, or greater, of the anti-tumor activity of a reference antibody as shown in Tables 1-4 when evaluated under the same assay conditions to measure the anti-tumor activity in vivo.
  • an anti-tumor antibody exhibits improved activity, i.e., greater than 100% activity, compared to the reference antibody.
  • an EphA2 antibody in accordance with the disclosure may be an antibody fragment, e.g., a Fv, Fab, Fab’, scFv, diabody, or F(ab’) 2 fragment.
  • the antibody is a substantially full-length antibody, e.g., an IgG antibody or other antibody class or isotype as defined herein.
  • Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells.
  • an EphA2 antibody according to the present disclosure that is administered to a patient is an IgG of the IgG1 subclass.
  • such an antibody is an IgG of the IgG2, IgG3, or IgG4 subclass.
  • such an antibody is an IgM.
  • such an antibody has a lambda light chain constant region.
  • such an antibody has a kappa light chain constant region.
  • an EphA2 antibody in accordance with the present disclosure is in a monovalent format.
  • the tumor-targeting antibody is in a fragment format, e.g., a Fv, Fab, Fab’, scFv, diabody, or F(ab’) 2 fragment.
  • EphA2 antibodies disclosed herein, including antibody fragments, of the present disclosure comprises an Fc region with effector function, e.g., exhibits antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), and/or complement- dependent cytotoxicity (CDC).
  • the Fc region may be an Fc region engineered to alter one or more functional properties of the antibody, such as serum half-life, complement fixation, Fc receptor binding, and/or ADCC.
  • an Fc region can comprise additional mutations to increase or decrease effector functions, i.e., the ability to induce certain biological functions upon binding to an Fc receptor expressed on an immune cell.
  • Immune cells include, but are not limited to, monocytes, macrophages, neutrophils, dendritic cells, eosinophils, mast cells, platelets, B cells, large granular lymphocytes, Langerhans’ cells, natural killer (NK) cells, and cytotoxic T cells.
  • an Fc region described herein can include additional modifications that modulate effector function.
  • Fc region amino acid mutations that modulate an effector function include, but are not limited to, one or more substitutions at positions 228, 233, 234, 235, 236, 237, 238, 239, 243, 265, 269, 270, 297, 298, 318, 326, 327, 329, 330, 331, 332, 333, and 334 (EU numbering scheme) of an Fc region.
  • Illustrative substitutions that decrease effector functions include the following: position 329 may have a mutation in which proline is substituted with a glycine or arginine or an amino acid residue large enough to destroy the Fc/Fc ⁇ receptor interface that is formed between proline 329 of the Fc and tryptophan residues Trp 87 and Trp 110 of Fc ⁇ RIII. Additional illustrative substitutions that decrease effector functions include S228P, E233P, L235E, N297A, N297D, and P331S.
  • L234A and L235A of a human IgG1 Fc region may also be present, e.g., L234A and L235A of a human IgG1 Fc region; L234A, L235A, and P329G of a human IgG1 Fc region; S228P and L235E of a human IgG4 Fc region; L234A and G237A of a human IgG1 Fc region; L234A, L235A, and G237A of a human IgG1 Fc region; V234A and G237A of a human IgG2 Fc region; L235A, G237A, and E318A of a human IgG4 Fc region; and S228P and L236E of a human IgG4 Fc region, to decrease effectors functions.
  • substitutions that increase effector functions include, e.g., E333A, K326W/E333S, S239D/I332E/G236A, S239D/A330L/I332E, G236A/S239D/A330L/I332E, F243L, G236A, and S298A/E333A/K334A.
  • the Fc mutations include P329G, L234A, L235A, or a combination thereof. Descriptions of amino acid mutations in an Fc region that can increase or decrease effector functions can be found in, e.g., Wang et al., Protein Cell.
  • an Fc region may have one or more amino acid substitutions that modulate ADCC, e.g., substitutions at positions 298, 333, and/or 334 of the Fc region, according to the EU numbering scheme.
  • S298A, E333A, and K334A can be introduced to an Fc region to increase the affinity of the Fc region to Fc ⁇ RIIIa and decrease the affinity of the Fc region to Fc ⁇ RIIa and Fc ⁇ RIIb.
  • An Fc region can also comprise additional mutations to increase serum half-life. Through enhanced binding to the neonatal Fc receptor (FcRn), such mutations in an Fc region can improve pharmacokinetics of the antibody.
  • substitutions in an Fc region that increase the serum half-life of an antibody include, e.g., M252Y/S254T/T256E, T250Q/M428L, N434A, N434H, T307A/E380A/N434A, M428L/N434S, M252Y/M428L, D259I/V308F, N434S, V308W, V308Y, and V308F.
  • Descriptions of amino acid mutations in an Fc region that can increase the serum half-life of an antibody can be found in, e.g., Dumet et al., MAbs.26:1-10, 2019; Booth et al., MAbs.
  • an antibody of the disclosure may be chemically modified (e.g., one or more chemical moieties can be attached to the antibody) or be modified, e.g., produced in cell lines and/or in cell culture conditions to alter its glycosylation (e.g., hypofucosylation, afucosylation, or increased sialylation), to alter one or more functional properties of the antibody.
  • the antibody can be linked to one of a variety of polymers, for example, polyethylene glycol.
  • an antibody may comprise mutations to facilitate linkage to a chemical moiety and/or to alter residues that are subject to post-translational modifications, e.g., glycosylation.
  • an EphA2 antibody described herein comprise an Fc region having altered glycosylation that increases the ability of the antibody to recruit NK cells and/or increase ADCC.
  • the Fc region comprises glycan containing no fucose (i.e., the Fc region is afucosylated).
  • Afucosylated antibodies can be produced using cell lines that express a heterologous enzyme that depletes the fucose pool inside the cell (e.g., GlymaxX ® by ProBioGen AG, Berlin, Germany). Non-fucosylated antibodies can also be produced using a host cell line in which the endogenous ⁇ -1,6-fucosyltransferase (FUT8) gene is deleted. See Satoh, M. et al., “Non-fucosylated therapeutic antibodies as next-generation therapeutic antibodies,” Expert Opinion on Biological Therapy, 6:11, 1161-1173, DOI: 10.1517/14712598.6.11.1161. [0199] In some embodiments, an EphA2 antibody is constructed as a multivalent antibody.
  • an EphA2 antibody is constructed as a tetravalent molecule, comprising four EphA2 binding arms per molecule. Such constructs exhibit increased ADCC activity, as well as increased binding to tumor cells a measured by flow cytometry.
  • an EphA2 antibody of the present disclosure is employed in a bispecific or multi-specific format, e.g., a tri-specific format.
  • the antibody may be incorporated into a bispecific or multi-specific antibody that comprises a further binding domain that binds to the same or a different antigen.
  • the formats can vary elements such as the number of binding arms, the format of each binding arm (e.g., Fab, scFv, scFab, or VH-only), the number of antigen binding domains present on the binding arms, the connectivity and geometry of each arm with respect to each other, the presence or absence of an Fc domain, the Ig class (e.g., IgG or IgM), the Fc subclass (e.g., hIgG1, hIgG2, or hIgG4), and any mutations to the Fc (e.g., mutations to reduce or increase effector function or extend serum half-life).
  • the Ig class e.g., IgG or IgM
  • the Fc subclass e.g., hIgG1, hIgG2, or hIgG4
  • any mutations to the Fc e.g., mutations to reduce or increase effector function or extend serum half-life.
  • Illustrative antigens that can be targeted by a further binding domain in a bispecific or multi- specific antibody that comprises an antigen binding domain of an EphA2 antibody described herein include, but are not limited to, antigens on T cells to enhance T cell engagement and/or activate T cells.
  • Illustrative examples of such an antigen include, but are not limited to, CD3, CD2, CD4, CD5, CD6, CD8, CD28, CD40L, CD44, IL-15R ⁇ , CD122, CD132, or CD25.
  • the antigen is CD3. In some embodiments, the antigen is in a T cell activating pathway, such as a 4-1BB/CD137, 4- 1BBL/CD137L, OX40, OX40L, GITRL, GITR, CD27, CD70, CD28, ICOS, HVEM, or LIGHT antigen.
  • an EphA2 antibody is incorporated into a bispecific or multi-specific antibody that comprises a binding domain that binds to a T-cell antigen. These bispecific antibodies or multi-specific antibodies can direct T cells to attach and lyse targeted tumor cells, i.e., the EphA2 expressing tumor cells.
  • the bispecific or multispecific antibody comprises a binding domain that binds to CD3. In some embodiments, the bispecific or multispecific antibody comprises a binding domain that binds to human CD3 comprising the anti-tumor antibodies described herein.
  • Table 9 provides specific examples of anti-CD3 binding arms that can be combined with any of the anti-EphA2 antibodies described herein.
  • Fig. 53 provides examples of a variety of formats according to which anti-EphA2/ anti-CD3 bispecific constructs that can be generated.
  • Table 9 CD3 heavy chain (VH) and light chain (VL) sequences.
  • FIG.54 shows treatment of mice carrying the tumors formed by PC3 tumor cells using an exemplary bispecific antibody led to tumor burden reduction and/or elimination of tumors in mice.
  • Said bispecific antibody was generated using a 1+1 (Fab-)(scFv-)Fc format (shown in FIG.53) and the CD3 arm of which comprises the VH/VL sequence of AB-008707.
  • Additional antigens that can be targeted by a further binding domain in a bispecific or multi- specific antibody that comprises an antigen binding domain of an EphA2 antibody described herein, include, but are not limited to, antigens on NK cells to activate or inhibit NK cell pathways.
  • NK cell receptors such as activating human Killer Immunoglobulin-like Receptor (KIR) family members, activating Ly49 family members, CD94-NKG2C/E/H heterodimeric receptors, NKG2D, SLAM family receptors including 2B4/CD244, CRACC/SLAMF7, NTB-A/SLAMF6, Fc gamma RIIIA/CD16a, CD27, CD100/Semaphorin 4D, CD160, natural cytotoxicity receptors, including NKp30, NKp44, and NKp46, DNAM-1/CD226, IL-2 receptor subunit beta (IL-2RB), IL-2 receptor subunit gamma (IL-2RG), 4- 1BB/CD137, and CRTAM.
  • KIR human Killer Immunoglobulin-like Receptor
  • Ly49 CD94-NKG2C/E/H heterodimeric receptors
  • NKG2D SLAM family receptors including 2B4/CD244, CRACC
  • an antigen include inhibiting NK cell receptors such as inhibiting human KIR family members, inhibiting Ly49 family members, CD94/NKG2A, TIGIT and CD96, sialic acid-binding Siglecs (Siglec-3, -7, and -9), ILT2/LILRB1, KLRG1, LAIR-1, CD161/NKR-P1A, and CEACAM-1.
  • an EphA2 antibody is incorporated into a bispecific or multi-specific antibody that comprises a binding domain from an agonist antibody that binds to 4-1BB.
  • the 4-1BB agonist antibody is a bispecific antibody that is capable of binding to both EphA2 and 4-1BB.
  • the term “4-1BB engager,” refers to the portion of a molecule (e.g., a bispecific antibody capable of binding to both 4-1BB and EphA2) that binds to 4-1BB.
  • the 4-1BB engager is an antibody or an antibody fragment (e.g., scFv) that binds to 4-1BB.
  • the 4-1BB engager is a multimeric 4-1BB ligand (“4-1BBL”), for example, a 4-1BBL trimer.
  • the bispecific antibody comprises one or more scFv fragments of an anti-4-1BB antibody and an EphA2 antibody disclosed herein.
  • the 4-1BB agonist antibody is a trispecific antibody.
  • bispecific and trispecific antibody constructs are described in US 20190010248, FIG.1; WO2020025659, FIG.1; Berezhnoy A. et al., Converting PD-L1-induced T-lymphocyte Inhibition into CD137-mediated Costimulation via PD-L1 x CD137 Bispecific DART ® Molecules. Poster presented at 30 th EORTC/AACR/NCI Symposium, November 13–16, 2018, Dublin, Ireland, Compte, M. et al., A tumor-targeted trimeric 4-1BB-agonistic antibody induces potent tumor-targeting immunity without systemic toxicity.
  • Non-limiting examples of the scFv of the anti 4-1BB antibodies that can be used in the fusion proteins are shown in Table 10.
  • Exemplary linkers that can be used to connect the heavy chain or light chain of the EphA2 antibody and the 4-1BB ligand domains in the fusion are shown in Table 14.
  • Various fusion proteins comprising the 4-1BBL and the EphA2 antibodies are shown in Table 14.
  • CH123 refers to an IgG heavy chain constant region comprising CH1-CH2-hinge-CH3.
  • Table 12 Additional 4-1BB antibody sequences suitable for use in generating bispecific constructs that are capable of binding to both EphA2 and 4-1BB are provided in Table 12.
  • Table 12.4-1BB antibody sequences suitable for generating bispecific constructs [0212] As shown in FIG.49, one exemplary bispecific antibody that comprises two scFv fragments of anti-4-1BB antibody linked to the HC of the EphA2 antibody AB-010361 showed capability of reducing tumor growth in mice carrying tumors formed from CT26 cells.
  • the fusion molecule comprises a silenced human IgG1 with three human 4-1BB ligand ectodomains attached via flexible linkers.
  • 4-1BBL fusion molecules can be utilized with the tumor-targeting antibodies described herein, see Zhang et al., Targeted and Untargeted CD137L Fusion Proteins for the Immunotherapy of Experimental Solid Tumors, Clin Cancer Res., 2758-2767 (2007), FIG. 1; (Kermer et al., Combining Antibody-Directed Presentation of IL-15 and 4-1BBL in a Trifunctional Fusion Protein for Cancer Immunotherapy, Mol Cancer Ther, 112-121 (2014), FIG.1.
  • an EphA2 antibody is incorporated into a fusion molecule comprising one or more 4-1BB ligands (4-1BBL).
  • a trimer of 4-1BBL is C-terminally fused to either the light chain or heavy chain of an EphA2 antibody.
  • one or more individual 4-1BBL domains are connected via linkers, with one of the domains additionally fused to the EphA2 antibody via a linker.
  • the 4-1BBL domains comprise entire ECD portion of the molecule or truncated forms that can still bind and activate 4-1BB. See WO2019086499, FIGs.1-3.
  • Non-limiting examples of the 4-1BBL domains that can be used in the fusion proteins are shown in Table 13.
  • Exemplary linkers that can be used to connect the heavy chain or light chain of the EphA2 antibody and the 4-1BB ligand domains in the fusion are shown in Table 14.
  • Various fusion proteins comprising the 4-1BBL and the EphA2 antibodies are shown in Table 14.
  • Table 13.4-1BBL domains used in the fusion constructs Note: Part names are comprised of the 4-1BBL domain, number of domains, and length of linker between domains.
  • Table 14.4-1BB fusion constructs *Terminology is as follows, using “h42BBL(THD)3-2” as an illustrative example: 1.
  • 41BBL stand for 4-1BB ligand (native sequence) 3.
  • THD stand for "TNF homology domain" portion of 41BBL. In instances where a number range in parentheses after 41BBL, e.g., h41BBL(71-248)3-10, refers to that residue numbers 71-248 of the 4-1BB ligand were used. 4.
  • “3” refers to three copies connected by polypeptide linker 5.
  • “-2” typically refers to the length of the linker used to connect the ligands together.
  • h41BBL(THD)3-2 represent h41BBL(THD) + GG + h41BBL(THD) + GG+ h41BBL(THD);
  • h41BBL(71-248)3-10 represents h41BBL(71-248) + (GGSGG)2 (SEQ ID NO: 781) + h41BBL(71-248) + (GGSGG)2 (SEQ ID NO: 781) + h41BBL(71-248) [0215]
  • the tumor-targeting antibody is conjugated to one or more TLR agonists.
  • the tumor-targeting antibody conjugated to a TLR agonist is a bispecific or multispecific antibody.
  • the tumor-targeting antibody is a bispecific or multispecific antibody comprising an antigen binding domain of an antibody described herein that further comprises a TLR agonist.
  • a bispecific or multispecific antibody comprising an antigen binding domain of an antibody described herein further comprises a binding domain that binds to a checkpoint antigen, PD1, PDL1, CTLA-4, ICOS, PDL2, IDO1, IDO2, B7-H3, B7-H4, BTLA, HVEM, TIM3, GAL9, GITR, HAVCR2, LAG3, KIR, LAIR1, LIGHT, MARCO, OX-40, , SLAM, , 2B4, CD2, CD27, CD28, CD30, CD40, CD70, CD80, CD86, CD137, CD160, CD39, VISTA, TIGIT, CGEN-15049, 2B4, CHK 1, CHK2, A2aR, or a B-7 family ligand or its receptor.
  • a bispecific or multispecific antibody comprising an antigen binding domain of an antibody described herein further comprises a binding domain that targets a tumor- associated antigen.
  • tumor-associate antigens include, but are not limited to, EpCAM, HER2/neu, HER3/neu, G250, CEA, MAGE, proteoglycans, VEGF, VEGFR, EGFR, ErbB2, ErbB3, MET, IGF-1R, PSA, PSMA, EphA2, EphA3, EphA4, folate binding protein ⁇ V ⁇ 3-integrin, integrin ⁇ 5 ⁇ l HLA, HLA-DR, ASC, CD1 , CD2, CD4, CD6, CD7, CD8, CD11 , CD13, CD14, CD19, CD20, CD21 , CD22, CD23, CD24, CD30, CD33, CD37, CD40, CD41 , CD47, CD52, c-erb-2, CALLA, MHCII
  • a binding domain of an antibody described herein may be incorporated into a chimeric antigen receptor (CAR-T) construct, an engineered TCR-T cell construct, or a combined CAR-T/TCR-T construct comprising the complete TCR complex (see Hardy et al. “Implications of T cell receptor biology on the development of new T cell therapies for cancer, Immunotherapy Vol.12, No. 1. Published Online: 6 Jan 2020 https://doi.org/10.2217/imt-2019-0046).
  • Such constructs can be used to generate a modified immune cell such as a T-cell, NK-cell, or monocyte/macrophage comprising the binding domain of an antibody described herein.
  • a first-generation CAR joins a single-chain variable region from the antibody to a CD3zeta ( ⁇ ) intracellular signaling domain of a CD3 T-cell receptor through hinge and transmembrane domains.
  • the CAR may contain co-stimulating domains, e.g., a second or third generation CAR may include an additional one or two-co-stimulating domains, such as 4-1BB, CD28, or OX-40).
  • a CAR-containing cell e.g., a CAR-T cell
  • an inducible expression component such as a cytokine, e.g., IL-12 or IL-15 to increase activation of CAR-T cells and activate innate immune cells.
  • the tumor-targeting binding domain comprises all six CDRs (HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3) sequences from the individual antibodies disclosed in Tables 6 and 7.
  • the tumor-targeting binding domain comprises the VH and VL sequences from the individual antibodies disclosed in Table 8. [0221] In one embodiment of any of the above bispecific or multispecific antibody constructs, the tumor-targeting binding domain comprises all six CDRs (HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3) sequences from any one of antibodies AB-008873; AB-009805; AB-009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; AB-009817, AB- 010141, AB-010142, AB-010143, AB-010144, AB-010145, AB-010146, AB-010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-0101
  • the tumor-targeting binding domain comprises all six CDRs (HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3) sequences from AB-010361 or AB- 010699.
  • the tumor-targeting binding domain comprises the V H and V L sequences any one of AB-008873; AB- 009805; AB-009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; and AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB- 010146, AB-010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB-010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB-010364, AB- 010365, AB-010366, AB
  • the tumor-targeting binding domain comprises the V H and V L sequences of AB-010361 or AB-010699.
  • GENERATION OF ANTIBODIES EphA2 antibodies as disclosed herein are commonly produced using vectors and recombinant methodology well known in the art (see, e.g., Sambrook & Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; Ausubel, Current Protocols in Molecular Biology). Reagents, cloning vectors, and kits for genetic manipulation are available from commercial vendors.
  • nucleic acids encoding a V H and/or V L region, or fragment thereof, of any of the tumor-targeting antibodies as described herein; vectors comprising such nucleic acids and host cells into which the nucleic acids are introduced that are used to replicate the antibody-encoding nucleic acids and/or to express the antibodies.
  • nucleic acids may encode an amino acid sequence containing the V L and/or an amino acid sequence containing the V H of the tumor-targeting antibody (e.g., the light and/or heavy chains of the antibody).
  • the host cell contains (1) a vector containing a polynucleotide that encodes the V L amino acid sequence and a polynucleotide that encodes the V H amino acid sequence, or (2) a first vector containing a polynucleotide that encodes the V L amino acid sequence and a second vector containing a polynucleotide that encodes the VH amino acid sequence.
  • the invention provides a method of making an EphA2 antibody as described herein.
  • the method includes culturing a host cell as described in the preceding paragraph under conditions suitable for expression of the antibody.
  • the antibody is subsequently recovered from the host cell (or host cell culture medium).
  • Suitable vectors containing polynucleotides encoding antibodies of the present disclosure, or fragments thereof, include cloning vectors and expression vectors. While the cloning vector selected may vary according to the host cell intended to be used, useful cloning vectors generally can self- replicate, may possess a single target for a particular restriction endonuclease, and/or may carry genes for a marker that can be used in selecting clones containing the vector.
  • Expression vectors generally are replicable polynucleotide constructs that contain a nucleic acid of the present disclosure.
  • the expression vector can be replicable in the host cells either as episomes or as an integral part of the chromosomal DNA.
  • Suitable expression vectors include but are not limited to plasmids and viral vectors, including adenoviruses, adeno-associated viruses, retroviruses, and any other vector.
  • Suitable host cells for expressing an EphA2 antibody as described herein include both prokaryotic and eukaryotic cells.
  • an EphA2 antibody may be produced in bacteria, when glycosylation and Fc effector function are not needed. After expression, the antibody may be isolated from the bacterial cell paste in a soluble fraction and can be further purified.
  • the host cell may be a eukaryotic host cell, including eukaryotic microorganisms, such as filamentous fungi or yeast, including fungi and yeast strains whose glycosylation pathways have been “humanized,” resulting in the production of an antibody with a partially or fully human glycosylation pattern, vertebrate, invertebrate, and plant cells.
  • eukaryotic microorganisms such as filamentous fungi or yeast, including fungi and yeast strains whose glycosylation pathways have been “humanized,” resulting in the production of an antibody with a partially or fully human glycosylation pattern, vertebrate, invertebrate, and plant cells.
  • invertebrate cells include insect cells. Numerous baculoviral strains have been identified which may be used in conjunction with insect cells. Plant cell cultures can also be utilized as host cells.
  • vertebrate host cells are used for producing an EphA2 antibody of the present disclosure.
  • mammalian cell lines such as a monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293 cells as described, e.g., in Graham et al., J. Gen Virol.36:59,1977; baby hamster kidney cells (BHK); mouse sertoli cells (TM4 cells as described, e.g., in Mather, Biol. Reprod.
  • COS-7 monkey kidney CV1 line transformed by SV40
  • human embryonic kidney line (293 or 293 cells as described, e.g., in Graham et al., J. Gen Virol.36:59,1977
  • BHK baby hamster kidney cells
  • TM4 cells as described, e.g., in Mather, Biol. Reprod.
  • monkey kidney cells (CV1); African green monkey kidney cells (VERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TRI cells, as described, e.g., in Mather et al., Annals N.Y. Acad. Sci.383:44-68, 1982; MRC 5 cells; and FS4 cells may be used to express an tumor-targeting antibodies.
  • Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR- CHO cells (Urlaub et al., Proc. Natl.
  • Host cells of the present disclosure also include, without limitation, isolated cells, in vitro cultured cells, and ex vivo cultured cells.
  • isolated cells in vitro cultured cells, and ex vivo cultured cells.
  • an EphA2 antibody of the present disclosure is produced by a CHO cell line, e.g., the CHO-K1 cell line.
  • One or more expression plasmids can be introduced that encode heavy and light chain sequences.
  • an expression plasmid encoding a heavy chain disclosed herein, e.g., SEQ ID NO: 67, and an expression plasmid encoding a light chain disclosed herein, e.g., SEQ ID NO: 68 are transfected into host cells as linearized plasmids at a ratio of 1:1 in the CHO-K1 host cell line using reagents such as Freestyle Max reagent. Fluorescence-activated cell sorting (FACS) coupled with single cell imaging can be used as a cloning method to obtain a production cell line.
  • FACS Fluorescence-activated cell sorting
  • a host cell transfected with an expression vector encoding an EphA2 antibody of the present disclosure, or fragment thereof, can be cultured under appropriate conditions to allow expression of the polypeptide to occur.
  • the polypeptides may be secreted and isolated from a mixture of cells and medium containing the polypeptides. Alternatively, the polypeptide may be retained in the cytoplasm or in a membrane fraction and the cells harvested, lysed, and the polypeptide isolated using a desired method.
  • an EphA2 antibody of the present disclosure can be produced by in vitro synthesis (see, e.g., Sutro Biopharma biochemical protein synthesis platform).
  • a method of generating variants of an EphA2 antibody as disclosed herein is a method of generating variants of an EphA2 antibody as disclosed herein.
  • a construct encoding a variant of a V H CDR3 as described herein can be modified and the V H region encoded by the modified construct can be tested for binding activity to CT26 cells and/or in vivo tumor-targeting activity in the context of a V H region as described herein, that is paired with a V L region or variant region as described herein.
  • a construct encoding a variant of a V L CDR3 as described herein can be modified and the V L region encoded by the modified construct can be tested for binding to CT26 cells, or other tumor cells, and/or in vivo tumor-targeting activity efficacy.
  • Such an analysis can also be performed with other CDRs or framework regions and an antibody having the desired activity can then be selected.
  • TUMOR-TARGETING ANTIBODY CONJUGATES/ CO-STIMULATORY AGENTS [0233]
  • an EphA2 antibody of the present disclosure may be conjugated or linked to therapeutic, imaging/detectable moieties, or enzymes.
  • the tumor-targeting antibody may be conjugated to a detectable marker, a cytotoxic agent, an immunomodulating agent, an imaging agent, a therapeutic agent, an oligonucleotide, or an enzyme.
  • a detectable marker for conjugating or linking antibodies to a desired molecule are well known in the art.
  • the desired molecule may be linked to the antibody covalently or by non-covalent linkages.
  • the antibody is conjugated, either directly or via a cleavable or non- cleavable linker, to a cytotoxic moiety or other moiety that exerts their effects on critical cellular processes required for survival (“payload”) to form an antibody-drug conjugate (“ADC”).
  • ADC antibody-drug conjugate
  • the antibody is conjugated to an auristatin.
  • the ADC is an EphA2 antibody disclosed herein conjugated to a ZymeLink TM Auristatin (ZLA) payload.
  • ZLA ZymeLink TM ADC constructs
  • ZymeLink TM ADCs of the present disclosure comprise an EphA2 antibody conjugated to a ZLA having structure (1) (also referred to herein as “Compound 1”) via a linker L.
  • the ZymeLink TM ADCs have Formula (I): wherein: L is a cleavable linker; n is the drug-to-antibody ratio (DAR) and is an integer from 1 to 12, and Ab is the antibody. [0238] In some embodiments, the each of the n drugs in formula (I) is independently conjugated to the antibody Ab via one of n linkers L. [0239] In some embodiments, in the ZymeLink TM ADCs of general Formula (I), linker L is a protease-cleavable linker. [0240] In some embodiments, in the ZymeLink TM ADCs of Formula (I), linker L is a peptide- containing linker.
  • linker L comprises a dipeptide selected from Val-Lys, Ala-Lys, Phe-Lys, Val-Cit, Phe-Cit, Leu-Cit, Ile-Cit and Trp-Cit.
  • linker L in the ZymeLink TM ADCs of Formula (I) comprises a dipeptide and a stretcher.
  • linker L in ZymeLink TM ADCs of Formula (I) is conjugated to the antibody via a cysteine residue or a lysine residue on the antibody.
  • linker L in ADCs of Formula (I) is conjugated to the antibody via a lysine residue on the antibody.
  • n is an integer from 1 to 8.
  • n has a value from 2 to 8, e.g., from 2 to 6, from 3 to 7, or from 4 to 8. In terms of upper limits, n can be less than 12, e.g., less than 11, less than 10, less than 9, less than 8, less than 7, less than 6, less than 5, less than 4, or less than 3.
  • n can be greater than 2, e.g., greater than 3, greater than 4, greater than 5, greater than 6, greater than 7, greater than 8, greater than 9, greater than 10, or greater than 11. Larger values of n, e.g., greater than 12, are also contemplated.
  • Combinations of any of the foregoing embodiments for ZymeLink TM ADCs of Formula (I) are also contemplated and each combination forms a separate embodiment for the purposes of the present disclosure.
  • the ZymeLink TM ADCs of the present disclosure have Formula (II): wherein: n is the drug-to-antibody ratio (DAR) and is an integer from 1 to 12, and Ab is the antibody.
  • DAR drug-to-antibody ratio
  • the each of the n drugs in formula (II) is independently conjugated to the antibody Ab via one of n linkers L.
  • the carbonyl group of Formula (II) marked with an asterisk forms a peptide bond with the side chain amine group of a lysine residue on the antibody (Ab).
  • n is an integer from 1 to 8. In some embodiments, in the ADCs of general Formula (II), n has a value from 2 to 8, e.g., from 2 to 6, from 3 to 7, or from 4 to 8.
  • n can be less than 12, e.g., less than 11, less than 10, less than 9, less than 8, less than 7, less than 6, less than 5, less than 4, or less than 3.
  • n can be greater than 2, e.g., greater than 3, greater than 4, greater than 5, greater than 6, greater than 7, greater than 8, greater than 9, greater than 10, or greater than 11. Larger values of n, e.g., greater than 12, are also contemplated.
  • Linker L In the ADCs of the present disclosure, the antibody is linked to an auristatin analogue disclosed herein by a linker L.
  • Linkers are bifunctional or multifunctional moieties capable of linking one or more drug molecules to an antibody.
  • a linker may be bifunctional (or monovalent) such that it links a single drug to a single site on the antibody, or it may be multifunctional (or polyvalent) such that it links more than one drug molecule to a single site on the antibody.
  • Linkers capable of linking one drug molecule to more than one site on the antibody may also be multifunctional.
  • Certain linkers useful in the present disclosure can be up to 30 carbon atoms in length.
  • the linkers can each independently be from 5 to 20 carbon atoms in length.
  • bonds used to link the linker to the cytotoxic agent and antibody of the present disclosure include, but are not limited to, amides, amines, esters, carbamates, ureas, thioethers, thiocarbamates, thiocarbonate and thioureas.
  • bonds are useful in the provided ADCs.
  • Attachment of a linker to an antibody can be accomplished in a variety of ways, such as through surface lysines on the antibody, reductive coupling to oxidized carbohydrates on the antibody, or through cysteine residues on the antibody liberated by reducing interchain disulfide linkages.
  • attachment of a linker to an antibody may be achieved by modification of the antibody to include additional cysteine residues (see, for example, U.S. Patent Nos. 7,521,541; 8,455,622 and 9,000,130) or non-natural amino acids that provide reactive handles, such as selenomethionine, p-acetylphenylalanine, formylglycine or p-azidomethyl-L-phenylalanine (see, for example, Hofer et al., Biochemistry, 48:12047-12057 (2009); Axup et al., PNAS, 109:16101-16106 (2012); Wu et al., PNAS, 106:3000-3005 (2009); Zimmerman et al., Bioconj.
  • additional cysteine residues see, for example, U.S. Patent Nos. 7,521,541; 8,455,622 and 9,000,130
  • non-natural amino acids that provide reactive handles, such as selenomethionine,
  • Linkers include at least one functional group capable of reacting with the target group or groups on the antibody, and one or more functional groups capable of reacting with a target group on the drug. Suitable functional groups are known in the art and include those described, for example, in Bioconjugate Techniques (G.T. Hermanson, 2013, Academic Press).
  • Examples of target groups on the antibody to which a linker may be conjugated include the thiol groups of cysteine residues and the amine groups of lysine residues.
  • Non-limiting examples of functional groups for reacting with free cysteines or thiols include maleimide, haloacetamide, haloacetyl, activated esters such as succinimide esters, 4-nitrophenyl esters, pentafluorophenyl esters, tetrafluorophenyl esters, anhydrides, acid chlorides, sulfonyl chlorides, isocyanates and isothiocyanates.
  • maleimide haloacetamide
  • haloacetyl activated esters such as succinimide esters, 4-nitrophenyl esters, pentafluorophenyl esters, tetrafluorophenyl esters, anhydrides, acid chlorides, sulfonyl chlorides, isocyanates and isothiocyanates.
  • self-stabilizing maleimides as described in Lyon et al., Nat. Biotechnol., 32:1059-1062 (2014).
  • Non-limiting examples of functional groups for reacting with free amines include activated esters (such as N-hydroxysuccinamide (NHS) esters, sulfo-NHS esters, imido esters such as Traut’s reagent, tetrafluorophenyl (TFP) esters and sulfodichlorophenyl esters), isothiocyanates, aldehydes and acid anhydrides (such as diethylenetriaminepentaacetic anhydride (DTPA)).
  • activated esters such as N-hydroxysuccinamide (NHS) esters, sulfo-NHS esters, imido esters such as Traut’s reagent, tetrafluorophenyl (TFP) esters and sulfodichlorophenyl esters
  • isothiocyanates such as N-hydroxysuccinamide (NHS) esters, sulfo-NHS esters, imido esters such
  • TSTU succinimido-1,1,3,3-tetra-methyluronium tetrafluoroborate
  • PyBOP benzotriazol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate
  • Other linkers include those having a functional group that allows for bridging of two interchain cysteines on the antibody, such as a ThioBridge ® linker (Badescu et al., Bioconjug. Chem., 25:1124–1136 (2014)), a dithiomaleimide (DTM) linker (Behrens et al., Mol.
  • a linker may comprise one or more linker components. Typically, a linker will comprise two or more linker components.
  • linker components include functional groups for reaction with the antibody, functional groups for reaction with the drug, stretchers, peptide components, self- immolative groups, self-elimination groups, hydrophilic moieties, and the like.
  • Various linker components are known in the art, some of which are described below.
  • Certain useful linker components can be obtained from various commercial sources, such as Pierce Biotechnology, Inc. (now Thermo Fisher Scientific Corporation, Waltham, MA) and Molecular Biosciences Inc. (Boulder, Colo.), or may be synthesized in accordance with procedures described in the art (see, for example, Toki et al., J. Org.
  • linker components include, but are not limited to, N-( ⁇ -maleimidopropyloxy)- N-hydroxy succinimide ester (BMPS), N-( ⁇ -maleimidocaproyloxy) succinimide ester (EMCS), N- [® ⁇ maleimidobutyryloxy]succinimide ester (GMBS), 1,6-hexane-bis-vinylsulfone (HBVS), succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxy-(6-amidocaproate) (LC-SMCC), m- maleimidobenzoyl-N-hydroxysuccinimide ester (MBS), 4-(4-N-maleimidophenyl)butyric acid hydrazide (MPBH), succinimidyl 3-(bromoacetamido)propionate (SBAP), succinimidyl iodoacetate (SIA), succinimidyl
  • Additional examples include bis-maleimide reagents such as dithiobismaleimidoethane (DTME), bis-maleimido-trioxyethylene glycol (BMPEO), 1,4-bismaleimidobutane (BMB), 1,4 bismaleimidyl-2,3-dihydroxybutane (BMDB), bismaleimidohexane (BMH), bismaleimidoethane (BMOE), BM(PEG)2 and BM(PEG)3; bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as dithi
  • Suitable linkers typically are more chemically stable to conditions outside the cell than to conditions inside the cell, although less stable linkers may be contemplated in certain situations, such as when the drug is selective or targeted and has a low toxicity to normal cells.
  • Linkers may be “cleavable linkers” or “non-cleavable linkers.”
  • a cleavable linker is typically susceptible to cleavage under intracellular conditions, for example, through lysosomal processes. Examples include linkers that are protease-sensitive, acid-sensitive, reduction-sensitive or photolabile.
  • Non-cleavable linkers by contrast, rely on the degradation of the antibody in the cell, which typically results in the release of an amino acid-linker-toxin moiety.
  • linker L comprised by the ADCs of Formula (I) is a cleavable linker.
  • Suitable cleavable linkers include, for example, linkers comprising a peptide component that includes two or more amino acids and is cleavable by an intracellular protease, such as lysosomal protease or an endosomal protease.
  • a peptide component may comprise amino acid residues that occur naturally and/or minor amino acids and/or non-naturally occurring amino acid analogues, such as citrulline.
  • linker L comprised by the ADCs of Formula (I) may be a peptide- containing linker.
  • linker L comprised by the ADCs may be a dipeptide- containing linker, such as a linker containing valine-citrulline (Val-Cit) or phenylalanine-lysine (Phe- Lys).
  • suitable dipeptides for inclusion in linker L include Val-Lys, Ala-Lys, Me- Val-Cit, Phe-homoLys, Phe-Cit, Leu-Cit, Ile-Cit, Trp-Cit, Phe-Arg, Ala-Phe, Val-Ala, Met-Lys, Asn- Lys, Ile-Pro, Ile-Val, Asp-Val, His-Val, Met-(D)Lys, Asn-(D)Lys, Val-(D)Asp, NorVal-(D)Asp, Ala- (D)Asp, Me3Lys-Pro, PhenylGly-(D)Lys, Met-(D)Lys, Asn-(D)Lys, Pro-(D)Lys and Met-(D)Lys.
  • Cleavable linkers may also include longer peptide components such as tripeptides, tetrapeptides or pentapeptides. Examples include, but are not limited to, the tripeptides Met-Cit-Val, Gly-Cit-Val, (D)Phe-Phe-Lys and (D)Ala-Phe-Lys, and the tetrapeptides Gly-Phe-Leu-Gly, Gly-Gly-Phe-Gly and Ala-Leu-Ala-Leu.
  • linker L comprised by the ADCs may be a peptide-containing linker, where the peptide is between two and five amino acids in length, for example, between two and four amino acids in length.
  • cleavable linkers include disulfide-containing linkers, such as, N- succinimydyl-4-(2-pyridyldithio) butanoate (SPBD) and N-succinimydyl-4-(2-pyridyldithio)-2-sulfo butanoate (sulfo-SPBD).
  • Disulfide-containing linkers may optionally include additional groups to provide steric hindrance adjacent to the disulfide bond to improve the extracellular stability of the linker, for example, inclusion of a geminal dimethyl group.
  • Other suitable linkers include linkers hydrolyzable at a specific pH or within a pH range, such as hydrazone linkers.
  • Linkers comprising combinations of these functionalities may also be useful, for example, linkers comprising both a hydrazone and a disulfide are known in the art.
  • a further example of a cleavable linker is a linker comprising a ⁇ -glucuronide, which is cleavable by ⁇ -glucuronidase, an enzyme present in lysosomes and tumor interstitium (see, for example, De Graaf et al., Curr. Pharm. Des., 8:1391–1403 (2002)).
  • Cleavable linkers may optionally further comprise one or more additional components such as self-immolative and self-elimination groups, stretchers or hydrophilic moieties.
  • Self-immolative and self-elimination groups that find use in linkers include, for example, p- aminobenzyloxycarbonyl (PABC) and p-aminobenzyl ether (PABE) groups, and methylated ethylene diamine (MED).
  • PABC p- aminobenzyloxycarbonyl
  • PABE p-aminobenzyl ether
  • MED methylated ethylene diamine
  • Other examples of self-immolative groups include, but are not limited to, aromatic compounds that are electronically similar to the PABC or PABE group such as heterocyclic derivatives, for example 2-aminoimidazol-5-methanol derivatives as described in U.S. Patent No.7,375,078.
  • Stretchers that find use in linkers for ADCs include, for example, alkylene groups and stretchers based on aliphatic acids, diacids, amines or diamines, such as diglycolate, malonate, caproate and caproamide.
  • stretchers include, for example, glycine-based stretchers, polyethylene glycol (PEG) stretchers and monomethoxy polyethylene glycol (mPEG) stretchers.
  • PEG and mPEG stretchers also function as hydrophilic moieties.
  • components commonly found in cleavable linkers include, but are not limited to, SPBD, sulfo-SPBD, hydrazone, Val-Cit, maleidocaproyl (MC), MC-Val-Cit, MC-Val-Cit-PABC, Phe-Lys, MC-Phe-Lys, MC-Phe-Lys-PABC, maleimido triethylene glycolate (MT), MT-Val-Cit, MT- Phe-Lys, TFP and adipate (AD).
  • SPBD polyethylene glycol
  • mPEG stretchers monomethoxy polyethylene glycol
  • AD adipate
  • linker L included in the ADCs of the present disclosure is a peptide- based linker having Formula (V): wherein: Z is a linking group that joins the linker to a target group on the antibody; Str is a stretcher; AA 1 and AA 2 are each independently an amino acid, wherein AA 1 -[AA 2 ] m forms a protease cleavage site; X is a self-immolative group; s is 0 or 1; m is 1, 2, 3 or 4; o is 0, 1 or 2; # is the point of attachment to the antibody, and % is the point of attachment to the auristatin analogue.
  • V peptide- based linker having Formula (V): wherein: Z is a linking group that joins the linker to a target group on the antibody; Str is a stretcher; AA 1 and AA 2 are each independently an amino acid, wherein AA 1 -[AA 2 ] m forms a protease clea
  • m is 1, 2 or 3.
  • s is 1.
  • o is 0 (i.e., X is absent).
  • Z is where # is the point of attachment to the antibody, and * is the point of attachment to the remainder of the linker.
  • Z is a carbonyl group (-C(O)-).
  • Str is selected from: wherein: each R is independently H or C 1 -C 6 alkyl; each p is independently an integer from 2 to 10; each q is independently an integer from 1 to 10, $ is the point of attachment to Z, and * is the point of attachment to the remainder of the linker. [0275] In some embodiments, in Formula (V), Str is: where p, q, $ and * are as defined above. [0276] In some embodiments, in Formula (V), Str is: where $ and * are as defined above, p is an integer from 2 to 6, and q is an integer from 2 to 8.
  • AA1-[AA2]m is selected from Val-Lys, Ala-Lys, Phe-Lys, Val-Cit, Phe-Cit, Leu-Cit, Ile-Cit, Trp-Cit, Phe-Arg, Ala-Phe, Val-Ala, Met-Lys, Asn-Lys, Ile-Pro, Ile-Val, Asp-Val, His-Val, Met-(D)Lys, Asn-(D)Lys, Val-(D)Asp, NorVal-(D)Asp, Ala- (D)Asp, Me3Lys-Pro, PhenylGly-(D)Lys, Met-(D)Lys, Asn-(D)Lys, Pro-(D)Lys, Met-(D)Lys, Met- Cit-Val, Gly-Cit-Val, (D)Phe-Phe-Lys,
  • m is 1 (i.e., AA1-[AA2]m is a dipeptide).
  • AA1-[AA2]m is a dipeptide selected from Val-Lys, Ala-Lys, Phe-Lys, Val-Cit, Phe-Cit, Leu-Cit, Ile-Cit and Trp-Cit.
  • Z is a carbonyl group (-C(O)-); Str is wher $ e is the point of attachment to Z, * is the point of attachment to the remainder of the linker, p is an integer from 2 to 6, and q is an integer from 2 to 8; m is 1 and AA 1 -[AA 2 ] m is a dipeptide selected from Val-Lys, Ala-Lys, Phe-Lys, Val-Cit, Phe- Cit, Leu-Cit, Ile-Cit and Trp-Cit; s is 1; and o is 0.
  • Z is where # is the point of attachment to the antibody, and * is the point of attachment to the remainder of the linker; Str is , where $ is the point of attachment to Z, * is the point of attachment to the remainder of the linker, p is an integer from 2 to 6, and q is an integer from 2 to 8; m is 1 and AA 1 -[AA 2 ] m is a dipeptide selected from Val-Lys, Ala-Lys, Phe-Lys, Val-Cit, Phe- Cit, Leu-Cit, Ile-Cit and Trp-Cit; s is 1; and o is 0.
  • the linker included in the ZymeLink TM ADCs of the present disclosure has Formula (VI): where: * is the point of attachment to the antibody; Y is one or more additional linker components, or is absent; and D is the point of attachment to the auristatin analogue. [0283] In some embodiments, in the linker of Formula (VI), Y is absent. [0284] In certain embodiments, the linker included in the ZymeLink TM ADCs of the present disclosure has Formula (VII): (VII) where: * is the point of attachment to the antibody; Y is one or more additional linker components, or is absent; and D is the point of attachment to the auristatin analogue.
  • Y is absent.
  • the linker included in the ZymeLink TM ADCs of the present disclosure has Formula (VIII): where: * is the point of attachment to the antibody; Y is one or more additional linker components, or is absent, and D is the point of attachment to the auristatin analogue.
  • Y is absent.
  • the antibody is conjugated to a microtubule inhibitor that induces apoptosis in cells undergoing mitosis by, for example, causing cell cycle arrest at G2/M.
  • microtubule inhibitors that can be used include maytansine derivatives (DM1/DM4), or auristatins (MMAE/MMAF) and variants thereof, such as monomethyl auristatin D, PF-06380101, duostatin5, AS269, Tap18Hr1, AGD-0182, HPA-Auristatin F.
  • the payload is a tubulin-targeting agent, for example, hemiasterlin, tubulysin, or eribulin.
  • the payloads are DNA-damaging payloads, which include enediynes (calicheamicin), duocarmycin derivatives, pyrrolobenzodiazepine dimers (PBD dimers), and indolinobenzodiazepine pseudo-dimers.
  • DNA-damaging payloads include enediynes (calicheamicin), duocarmycin derivatives, pyrrolobenzodiazepine dimers (PBD dimers), and indolinobenzodiazepine pseudo-dimers.
  • the antibody is conjugated to a cytotoxic agent including, but not limited to, e.g., ricin A chain, doxorubicin, daunorubicin, a maytansinoid, taxol, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, methotrexact, actinomycin, a diphtheria toxin, extotoxin A from Pseudomonas, Pseudomonas exotoxin40, abrin, abrin A chain, modeccin A chain, alpha sarcin, gelonin, mitogellin, restrictocin, cobran venom factor, a ribonuclease, engineered Shiga toxin, phenomycin, enomycin, curicin, crotin, calicheamicin
  • a cytotoxic agent
  • the antibody may be linked to an agent such as an enzyme inhibitor, a proliferation inhibitor, a lytic agent, a DNA or RNA synthesis inhibitors, a membrane permeability modifier, a DNA metabolite, a dichloroethylsulfide derivative, a protein production inhibitor, a ribosome inhibitor, or an inducer of apoptosis.
  • the antibody is conjugated to a drug such as a topoisomeriase inhibitor, e.g., a topoisomeraise I inhibitor.
  • Topoisomeraise I inhibitors include but are not limited to quinoline alkaloids (SN-38, DXd).
  • the antibody is conjugated to a cancer chemotherapeutic agent, as described below.
  • the antibody is conjugated to one or more of the cytotoxic and/or anti- mitotic compounds as disclosed in WO2014144871A1 and WO2016041082A1, the entire content of both applications are herein incorporated by reference.
  • an EphA2 antibody as described herein is joined to a molecule that facilitates transport of the antibody across a biological membrane, e.g., by enhancing penetration of the membrane, facilitating protein translocation across membranes.
  • the antibody may be linked to a cell penetration agent, such as a cell-penetrating peptide.
  • cell penetrating peptides examples include TAT, penetrating, polyarginine molecules, Kunitz domain-derived peptides, e.g., angiopep-2, SynB, buforin, transportan, amphiphathic peptides and others.
  • the antibody may be conjugated with a cationic molecule such as a polyamine.
  • the antibody may be conjugated to an agent that facilitates transport across the blood brain barrier, e.g., transcytosis.
  • the antibody may be conjugated to an agent that binds to endothelial cell receptors that are internalized, e.g., transferrin receptor, insulin receptor, insulin-like growth factor receptor, or a low-density lipoprotein receptor, and the like.
  • the antibody may be conjugated to a toxin facilitating entry of the antibody into the cytoplasm, e.g., Shiga toxin.
  • an EphA2 antibody as described herein can be conjugated to an engineered toxin body (ETBs) to facilitate internalization of the antibody into a cell.
  • ETBs engineered toxin body
  • an EphA2 antibody described herein is conjugated or administered with a polypeptide immunomodulating agent, e.g., an adjuvant.
  • immunomodulating agents include, but are not limited to, cytokines (e.g., transforming growth factor- ⁇ (TGF ⁇ )), growth factors, lymphotoxins, tumor necrosis factor (TNF), hematopoietic factors, interleukins (e.g., interleukin-1 (IL- 1), IL-2, IL-3, IL-6, IL-10, IL-12, IL-15, an IL-15/IL-15R ⁇ , e.g., sushi domain, complex, IL-18, and IL-21), colony stimulating factors (e.g., granulocyte-colony stimulating factor (G-CSF) and granulocyte macrophage-colony stimulating factor (GM-CSF), interferons (e.g., interferon- ⁇ , - ⁇ or - ⁇ , erythro
  • G-CSF gran
  • the antibody is linked or administered with a compound that stimulates the innate immune system, such as an adjuvant, a Toll-like receptor (TLR) agonist, a C-type lectin receptor (CLR) agonist, a retinoic acid-inducible gene I-like receptor (RLR) agonist, a saponin, a polysaccharide such as chitin, chitosan, ⁇ -glucan, an ISCOM, QS-21, a stimulator of interferon genes (STING) agonist, or another immunopotentiating agent.
  • TLR Toll-like receptor
  • CLR C-type lectin receptor
  • RLR retinoic acid-inducible gene I-like receptor
  • an EphA2 antibody described herein is conjugated to or administered with an IL-15 receptor agonist, such as an IL-15 fusion construct, an IL-15:IL-15R ⁇ fusion construct or a single-chain IL-15:IL-15R ⁇ (sushi) fusion construct.
  • an IL-15 receptor agonist such as an IL-15 fusion construct, an IL-15:IL-15R ⁇ fusion construct or a single-chain IL-15:IL-15R ⁇ (sushi) fusion construct.
  • the tumor-targeting antibody conjugated to an IL-15 receptor agonist is a bispecific or multispecific antibody.
  • the antibody is a bispecific or multispecific antibody comprising an antigen binding domain described herein that further comprises an IL-15 receptor agonist.
  • an EphA2 antibody described herein is administered with a single-chain IL-15:IL-15R ⁇ (sushi) fusion construct.
  • an EphA2 antibody is administered with a polymer-conjugated IL-15 construct, such as NKTR-255.
  • the IL-15:IL-15R ⁇ single chain constructs can be administered to a subject comprising a therapeutically effective dose, for example in the range of less than 0.01 mg/kg body weight to about 25 mg/kg body weight, or 0.1 – 10 mg/kg, or in the range 1 mg – 2 g per patient, or approximately 50 mg – 1000 mg / patient.
  • the single-chain IL-15 fusion construct comprises IL-15 joined to IL- 15R ⁇ (sushi) with a polypeptide linker.
  • the single-chain IL-15 fusion construct is joined via a polypeptide linker to another protein, such as an Fc for long half-life. See, for example, FIG.9B in WO2018071919A1 (corresponding to U.S. Patent No.10550185).
  • the IL-15 is joined or fused to the N-terminus of the heavy chain of an Fc, and IL-15R ⁇ (sushi) is joined or fused to the other Fc heavy chain N-terminus, using a heavy chain heterodimerization technology to form the desired hybrid Fc. See, for example, FIG.9A in WO2018071919A1.
  • the IL-15:IL-15R ⁇ (sushi) single chain constructs are fused to the C- terminus of an antibody light chain, or the C-terminus of an antibody heavy chain, in both cases producing a molecule with two tumor-targeting binding sites (the Fab arms), and two IL15:IL15R ⁇ units. Illustrative configurations of the fusion construct is shown in FIG.36.
  • one copy of an IL15:IL15R ⁇ fusion construct is fused to an EphA2 antibody, thereby producing an antibody molecule comprising two tumor-targeting binding sites (the Fab arms) and only one IL15:IL15R ⁇ unit, for example using a knob-in-holes approach to heavy chain heterodimerization, or other heterodimerization technology.
  • the IL-15:IL-15R ⁇ (sushi) fusion constructs or the antibodies comprising the fusion constructs comprise a low affinity IL-15 variant having improved pharmacokinetics (PK).
  • the IL-15:IL-15R ⁇ (sushi) fusion constructs comprise a high affinity IL-15 variant having increased agonist activity.
  • the high affinity IL-15 variant has an N72D mutation.
  • the high affinity variant is fused to a dimeric IL-15R ⁇ sushi domain-IgG1 Fc fusion protein.
  • the IL-15:IL-15R ⁇ (sushi) fusion construct is ALT-803. See Liu B, et al. (November 2016). “A Novel Fusion of ALT-803 (Interleukin (IL)-15 Superagonist) with an Antibody Demonstrates Antigen-specific Antitumor Responses”. The Journal of Biological Chemistry. 291 (46): 23869–23881. doi:10.1074/jbc.M116.733600.
  • antibodies comprising the IL15:IL15R ⁇ fusion construct comprise one or more mutations in the Fc region described herein, for example E333A, K326W/E333S, S239D/I332E/G236A, S239D/A330L/I332E, G236A/S239D/A330L/I332E, F243L, G236A, and S298A/E333A/K334A.
  • antibodies comprising the IL15:IL15R ⁇ fusion comprise one or more mutations in the Fc region that increase binding of the antibody to tumor cells, for example the mutations P329G, L234A, L235A, or a combination thereof.
  • antibodies comprising the IL15:IL15R ⁇ fusion construct comprises one or more sequences shown in Table 15.
  • the fusion protein comprises or consists of SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, and SEQ ID NO: 92.
  • the fusion protein comprises or consists of SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, and SEQ ID NO: 93.
  • an EphA2 antibody described herein is conjugated to or administered with an IL-2 receptor agonist.
  • the tumor-targeting antibody that is conjugated to an IL-2 receptor agonist is a bispecific or multispecific antibody.
  • the antibody is a bispecific or multispecific antibody comprising an antigen binding domain of an antibody described herein and an IL-2 receptor agonist.
  • the IL-2 receptor agonist is pegylated IL-2.
  • an EphA2 antibody described herein is conjugated to or administered with a construct that can act as a trap for transforming growth factor- ⁇ (TGF ⁇ ).
  • TGF ⁇ trap comprises the extracellular domain (ECD) of TGF ⁇ .
  • the TGF ⁇ trap comprises the extracellular domain (ECD) of TGF ⁇ RII.
  • the TGF ⁇ trap is in the form of a bispecific antibody (see US2018/0118832A1, FIG.1).
  • the TGF ⁇ RII ECD can preferably trap TGF ⁇ 1, and its low affinity to TGF ⁇ 2 may mitigate potential cardiac toxicity.
  • an EphA2 antibody described herein comprises an extracellular domain (ECD) of the TGF ⁇ Receptor fused to the C-terminus of the heavy chain or to the C-terminus of the light chain.
  • the TGF ⁇ trap is a single trap construct.
  • the single TGF ⁇ trap is a bispecific tumor-targeting TGF ⁇ trap comprising a TGF ⁇ RII ECD fused to any one of the antibodies disclosed herein via a flexible linker to the C-terminus of the heavy chain or to the C-terminus of the light chain.
  • the TGF ⁇ trap is a tandem trap construct.
  • the tandem TGF ⁇ trap comprises an IgG fused to two TGF ⁇ RII ECDs. In some embodiments, the tandem TGF ⁇ trap comprises two TGF ⁇ 2RII ECDs. In some embodiments, the two TGF ⁇ 2RII ECDs are fused in series and are linked by a short linker (for example L10 or L25). In some embodiments, the two TGF ⁇ 2RII ECDs are fused directly in series without a linker (L0). In some embodiments, the tandem TGF ⁇ RII ECDs are fused to the C-terminus of the heavy chain (HC-Cter), and the heavy chains were designed as an asymmetric pair such that the tandem trap is on only one heavy chain.
  • HC-Cter heavy chain
  • the asymmetric pair of heavy chains comprise knob-in-hole mutation that promote pairing of the heavy chains.
  • one heavy chain comprises the amino acid substitutions T366S+L368A+Y407V (and optionally Y349C), and the other heavy chain comprises the amino acid substitution T336W (and optionally S354C).
  • the asymmetric single heavy chain C-ter fusion improves steric access of the Fc region to Fc gamma receptors and thereby improve function.
  • the tandem TGF ⁇ trap is fused to the C-terminus of the light chain (LC-Cter), such that both light chains comprise two TGF ⁇ RII ECDs.
  • the net molecule exhibits twice the TGF ⁇ trapping capacity per molecule, and therefore may exhibit improved function.
  • the bispecific TGF ⁇ trap construct comprises human variable regions.
  • the bispecific TGF ⁇ trap construct comprises a IgG1 or IgG2 constant region.
  • the bispecific TGF ⁇ trap construct comprises a human IgG1 constant region.
  • the bispecific TGF ⁇ trap construct comprises a mouse IgG2a constant region.
  • the variable regions of the TGF ⁇ trap construct are fused in frame to the IgG constant regions.
  • Binding of the TGF ⁇ trap construct can be determined using, for example, an ELISA assay, as described in the Examples.
  • the ability of TGF ⁇ trap constructs to bind to target tumor cells can be determined, for example, using flow-cytometry, as described in the Examples.
  • the ability of TGF ⁇ trap constructs to engage and stimulate Fc-gamma receptor in the presence of target tumor cells can be determined using a reporter bioassay, as described in the Examples.
  • the ability of TGF ⁇ trap constructs to inhibit tumor growth can be determined, for example, in a syngeneic mouse model, as described in the Examples.
  • the antibody may be linked to a radionuclide, an iron-related compound, a dye, a fluorescent agent, or an imaging agent.
  • an antibody may be linked to agents, such as, but not limited to, metals; metal chelators; lanthanides; lanthanide chelators; radiometals; radiometal chelators; positron-emitting nuclei; microbubbles (for ultrasound); liposomes; molecules microencapsulated in liposomes or nanosphere; monocrystalline iron oxide nanocompounds; magnetic resonance imaging contrast agents; light absorbing, reflecting and/or scattering agents; colloidal particles; fluorophores, such as near-infrared fluorophores.
  • the EphA2 antibody is any one of AB- 008873; AB-009805; AB-009806; AB-009807; AB-009808; AB-009812; AB-009813; AB-009814; AB-009815; AB-009816; AB-009817, AB-010141, AB-010142, AB-010143, AB-010144, AB- 010145, AB-010146, AB-010147, AB-010148, AB-010149, AB-010150, AB-010151, AB-010152, AB-010357, AB-010358, AB-010359, AB-010360, AB-010361, AB-010362, AB-010363, AB- 010364, AB-010365, AB-010366, AB-010367, AB-010661, AB-010662,
  • the tumor-targeting binding domain comprises the V H and V L sequences of AB-010361 or AB-010699.
  • METHODS OF INDUCING AN IMMUNE RESPONSE [0311]
  • the EphA2 antibody is an antibody set forth in Tables 6-8, or a variant thereof as described above.
  • the antibody or variant thereof comprises a modified Fc region comprising mutations described herein.
  • the antibody comprises an Fc mutation that increases effect function selected from E333A, K326W/E333S, S239D/I332E/G236A, S239D/A330L/I332E, G236A/S239D/A330L/I332E, F243L, G236A, S298A/E333A/K334A, and P329G/L234A/L235A, or a combination thereof.
  • the antibody comprises a modified Fc region that is a-fucosylated.
  • the antibody is conjugated to or administered with an IL-15 receptor agonist, a TGF ⁇ trap, a TLR agonist, or an agonist anti-4-1BB antibody.
  • the antibody is a bispecific or multispecific antibody described herein.
  • An immune response induced by administration of an antibody as described herein can be either an innate or adaptive immune response.
  • the antibody activates an immune response directly, e.g., via binding of the antibody to a target tumor cell and engagement with an Fc receptor on an effector cell such that the effector cell is activated.
  • the antibody indirectly activates an immune response by inducing immune responses that are initiated by antibody binding to the target cell and an effector cell with subsequent induction of downstream immune responses.
  • the antibody activates monocytes, myeloid cells, and/or NK cells, e.g., macrophages, neutrophils, dendritic cells, mast cells, basophils, eosinophile, and/or NK cells. In some embodiments, the antibody activates T lymphocytes and/or B cells. TREATMENT OF CANCER [0313]
  • an EphA2 antibody as provided herein, or a variant thereof as described herein can be used and a therapeutic agent to treat cancer.
  • the antibody or variant thereof comprises a modified Fc region comprising mutations described herein.
  • the antibody comprises an Fc mutation that increases effector function selected from E333A, K326W/E333S, S239D/I332E/G236A, S239D/A330L/I332E, G236A/S239D/A330L/I332E, F243L, G236A, S298A/E333A/K334A, and P329G/L234A/L235A, or a combination thereof.
  • the antibody comprises a modified Fc region that is afucosylated.
  • the antibody is conjugated to or administered with an IL-15 receptor agonist, a TGF ⁇ trap, a TLR agonist, or an agonist anti-4-1BB antibody. In some embodiments, the antibody is a bispecific or multispecific antibody described herein.
  • the disclosure additionally provides methods of identifying subjects who are candidates for treatment with an EphA2 antibody having tumor-targeting effects.
  • the invention provides a method of identifying a patient who can benefit from treatment with an EphA2 antibody of the present disclosure.
  • the patient has tumor that expresses EphA2.
  • the patient has tumor that overexpresses EphA2.
  • the tumor sample is from a primary tumor.
  • the tumor sample is a metastatic lesion. Binding of antibody to tumor cells through a binding interaction with the EphA2 can be measured using any assay, such as immunohistochemistry or flow cytometry. In some embodiments, binding of antibody to at least 0.2%, 0.5%, or 1%, or at least 5% or 10%, or at least 20%, 30%, or 50%, of the tumor cells in a sample may be used as a selection criterion for determining a patient to be treated with an EphA2 antibody as described herein.
  • an EphA2 antibody disclosed herein can be used to treat several different cancers.
  • a cancer patient who can benefit from the treatment of the EphA2 antibody has a cancer that expresses EphA2.
  • a cancer patient who can benefit from the treatment of the EphA2 antibody has a cancer overexpressing EphA2.
  • the cancer is a carcinoma or a sarcoma.
  • the cancer is a hematological cancer.
  • the cancer is breast cancer, prostate cancer, testicular cancer, renal cell cancer, bladder cancer, ovarian cancer, cervical cancer, endometrial cancer, lung cancer, colorectal cancer, anal cancer, pancreatic cancer, gastric cancer, esophageal cancer, hepatocellular cancer, head and neck cancer, a brain cancer, e.g., glioblastoma, melanoma, or a bone or soft tissue sarcoma.
  • the cancer is acral melanoma.
  • the cancer is acute lymphoblastic leukemia, acute myeloid leukemia, adrenocortical carcinoma, astrocytoma, basal-cell carcinoma, bile duct cancer, bone tumor, brainstem glioma, cerebellar astrocytoma, cerebral astrocytoma, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumors, visual pathway and hypothalamic glioma, bronchial adenomas, Burkitt’s lymphoma, central nervous system lymphoma, cerebellar astrocytoma, chondrosarcoma, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloproliferative disorders, colon cancer, cutaneous T-cell lymphoma, desmoplastic small round cell tumor, endometrial cancer, ependymoma, epithelioid hemangioend
  • plasma cell neoplasia pleuropulmonary blastoma, primary central nervous system lymphoma, rectal cancer, renal cell carcinoma, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, Ewing sarcoma, Kaposi sarcoma, soft tissue sarcoma, uterine sarcoma, Sézary syndrome, non- melanoma skin cancer, melanoma,, small intestine cancer, squamous cell carcinoma, squamous neck cancer, stomach cancer, cutaneous T-Cell lymphoma, throat cancer, thymoma, thyroid cancer, transitional cell cancer of the renal pelvis and ureter, trophoblastic tumor, gestational, urethral cancer, uterine cancer, vaginal cancer, vulvar cancer, Waldenström macroglobulinemia, or Wilms tumor.
  • the cancer is lung cancer, e.g., non-small cell lung adenocarcinoma or squamous cell carcinoma; breast cancer, e.g., Triple- , ER/PR + Her2 - , ER/PR - Her2 + , or Triple - ; colorectal cancer, e.g., adenocarcinoma, mucinous adenocarcinoma, or papillary adenocarcinoma; esophageal cancer; stomach cancer; kidney cancer, e.g., kidney clear cell cancer; ovarian cancer, e.g., ovarian endometrioid carcinoma, ovarian mucinous cystadenocarcinoma, or ovarian serous cystadenocarcinoma; melanoma, e.g., acral melanoma, cutaneous melanoma, or mucosal melanoma; uterine or cervical cancer, adenocarcino
  • an EphA2 antibody disclosed herein can be used to treat a gastric cancer, ovarian cancer, or soft tissue sarcoma.
  • the EphA2 antibody e.g., AB- 008873
  • methods of the disclosure comprise administering an EphA2 antibody disclosed herein, or a variant thereof, as a pharmaceutical composition to a cancer patient in a therapeutically effective amount using a dosing regimen suitable for treatment of the cancer.
  • the composition can be formulated for use in a variety of drug delivery systems.
  • compositions for proper formulation can also be included in the compositions for proper formulation.
  • suitable formulations for use in the present disclosure are found, e.g., in Remington: The Science and Practice of Pharmacy, 21st Edition, Philadelphia, PA. Lippincott Williams & Wilkins, 2005.
  • the tumor-targeting antibody is provided in a solution suitable for administration to the patient, such as a sterile isotonic aqueous solution for injection.
  • the antibody is dissolved or suspended at a suitable concentration in an acceptable carrier.
  • the carrier is aqueous, e.g., water, saline, phosphate buffered saline, and the like.
  • compositions may contain auxiliary pharmaceutical substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, and the like.
  • auxiliary pharmaceutical substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, and the like.
  • the pharmaceutical compositions are administered to a patient in an amount sufficient to cure or at least partially arrest the disease or symptoms of the disease and its complications. An amount adequate to accomplish this is defined as a “therapeutically effective dose.”
  • a therapeutically effective dose is determined by monitoring a patient’s response to therapy. Typical benchmarks indicative of a therapeutically effective dose include the amelioration of symptoms of the disease in the patient.
  • An EphA2 antibody can be administered by any suitable means, including, for example, parenteral, intrapulmonary, and intranasal, administration, as well as local administration, such as intratumor administration.
  • Parenteral infusions include intramuscular, intravenous, intraarterial, intraperitoneal, or subcutaneous administration.
  • the antibody may be administered by insufflation.
  • the antibody may be stored at 10 mg/ml in sterile isotonic aqueous saline solution for injection at 4°C and is diluted in either 100 ml or 200 ml 0.9% sodium chloride for injection prior to administration to the patient.
  • the antibody is administered by intravenous infusion over the course of 1 hour at a dose of between 0.01 and 25 mg/kg.
  • the antibody is administered by intravenous infusion over a period of between 15 minutes and 2 hours.
  • the administration procedure is via sub- cutaneous bolus injection.
  • the dose of antibody is chosen to provide effective therapy for the patient and is in the range of less than 0.01 mg/kg body weight to about 25 mg/kg body weight or in the range 1 mg – 2 g per patient. Preferably the dose is in the range 0.1 – 10 mg/kg or approximately 50 mg – 1000 mg / patient.
  • the dose may be repeated at an appropriate frequency which may be in the range once per day to once every three months, or every six months, depending on the pharmacokinetics of the antibody (e.g., half- life of the antibody in the circulation) and the pharmacodynamic response (e.g., the duration of the therapeutic effect of the antibody).
  • the in vivo half-life of between about 7 and about 25 days and antibody dosing is repeated between once per week and once every 3 months or once every 6 months. In other embodiments, the antibody is administered approximately once per month.
  • the antibody may be stored at 10 mg/ml or 20 mg/ml in a sterile isotonic aqueous solution.
  • the solution can comprise agents such as buffering agents and stabilizing agents.
  • a buffering agent such as histidine is included to maintain a formulation pH of about 5.5. Additional reagents such as sucrose or alternatives can be added to prevent aggregation and fragmentation in solution and during freezing and thawing.
  • agents such as polysorbate 80 or an alternative can be included to lower surface tension and stabilizes the antibody against agitation-induced denaturation and air-liquid and ice-liquid surface denaturation.
  • the solution for injection is stored at 4°C and is diluted in either 100 ml or 200 ml 0.9% sodium chloride for injection prior to administration to the patient.
  • antibody for IV administration is formulated at a target concentration of 20 mg/mL in 20 mM histidine buffer, 8% (w/v) sucrose and 0.02% (w/v) polysorbate 80, pH 5.5.
  • An EphA2 antibody disclosed herein may be administered with one or more additional therapeutic agents, e.g., radiation therapy, chemotherapeutic agents and/or immunotherapeutic agents.
  • an EphA2 antibody can be administered in conjunction with an agent that targets an immune checkpoint antigen.
  • the agent is a biologic therapeutic or a small molecule.
  • the agent is a monoclonal antibody, a humanized antibody, a human antibody, a fusion protein or a combination thereof.
  • the agents inhibit, e.g., by blocking ligand binding to receptor, a checkpoint antigen that may be PD1, PDL1, CTLA-4, ICOS, PDL2, IDO1, IDO2, B7-H3, B7-H4, BTLA, HVEM, TIM3, GAL9, GITR, HAVCR2, LAG3, KIR, LAIR1, LIGHT, MARCO, OX-40, SLAM, , 2B4, CD2, CD27, CD28, CD30, CD40, CD70, CD80, CD86, CD137 (4-1BB), CD160, CD39, VISTA, TIGIT, a SIGLEC, CGEN-15049, 2B4, CHK1, CHK2, A2aR, B-7 family ligands or their receptors, or a combination thereof.
  • a checkpoint antigen that may be PD1, PDL1, CTLA-4, ICOS, PDL2, IDO1, IDO2, B7-H3, B7-H4, BTLA, HVEM, TIM
  • the agent targets PD-1, e.g., an antibody that blocks PD-L1 binding to PD-1 or otherwise inhibits PD-1.
  • the agent targets CTLA-4.
  • the agent targets LAG3.
  • the agent targets TIM3.
  • the agents target ICOS.
  • an EphA2 antibody can be administered in conjunction with a therapeutic antibody, such as an antibody that targets a tumor cell antigen.
  • therapeutic antibodies include as rituximab, trastuzumab, tositumomab, ibritumomab, alemtuzumab, atezolizumab, avelumab, durvalumab, pidilizumab, AMP-224, AMP-514, PDR001, cemiplimab, BMS-936559, CK- 301, epratuzumab, bevacizumab, elotuzumab, necitumumab, blinatumomab, brentuximab, cetuximab, daratumumab, denosumab, dinutuximab, gemtuzumab ibritumomab ipilimumab, nivolumab, obinutuzumab, ofatumumab, ado-trastuzumab, panitumumab, pembrolizuma
  • an EphA2 antibody can be administered in conjunction with a therapeutic antibody that binds an extracellular RNA-protein complex comprising polyadenylated RNA, such as the antibody designated ATRC-101, see WO2020168231 incorporated herein in its entirety.
  • an EphA2 antibody as described herein is administered with an agonist anti-4-1BB antibody such as urelumab (Bristol Meyers Squibb, BMS-663513, US7288638), utomilumab, (Pfizer, PF-05082566, WO2012145183), 1D8 and 5B9 (US20100279932), hu106-1, TABBY 101- TABBY 110 (WO2017205745, FIGS.
  • an agonist anti-4-1BB antibody such as urelumab (Bristol Meyers Squibb, BMS-663513, US7288638), utomilumab, (Pfizer, PF-05082566, WO2012145183), 1D8 and 5B9 (US20100279932), hu106-1, TABBY 101- TABBY 110 (WO2017205745, FIGS.
  • an EphA2 antibody is administered with a chemotherapeutic agent.
  • cancer chemotherapeutic agents include alkylating agents such as thiotepa and cyclophosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethylenethiophosphaoramide and trimethylolomelamine; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fo
  • paclitaxel and doxetaxel paclitaxel and doxetaxel; chlorambucil; gemcitabine; 6- thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; docetaxel, platinum; etoposide (VP- 16); ifosfamide; mitomycin C; mitoxantrone; vincristine; vinorelbine; navelbine; novantrone; teniposide; daunomycin; aminopterin; xeloda; ibandronate; CPT-11; topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO); retinoic acid derivatives such as bexarotene, alitretinoin; denileukin diftitox; esperamicins; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above
  • anti-hormonal agents that act to regulate or inhibit hormone action on tumors
  • anti- estrogens including for example tamoxifen, raloxifene, mifepristone, aromatase inhibiting 4(5)- imidazoles, 4-hydroxytamoxifen, trioxifene, keoxifene, LY 1 17018, onapristone, and toremifene (Fareston); and anti-androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; and pharmaceutically acceptable salts, acids or derivatives of any of the above.
  • cancer therapeutic agents include sorafenib and other protein kinase inhibitors such as afatinib, axitinib, crizotinib, dasatinib, erlotinib, fostamatinib, gefitinib, imatinib, lapatinib, lenvatinib, mubritinib, nilotinib, pazopanib, pegaptanib, ruxolitinib, vandetanib, vemurafenib, and sunitinib; sirolimus (rapamycin), everolimus and other mTOR inhibitors.
  • protein kinase inhibitors such as afatinib, axitinib, crizotinib, dasatinib, erlotinib, fostamatinib, gefitinib, imatinib, lapatinib, lenvatinib, mubritinib,
  • chemotherapeutic agents include topoisomerase I inhibitors (e.g., irinotecan, topotecan, camptothecin and analogs or metabolites thereof, and doxorubicin); topoisomerase II inhibitors (e.g., etoposide, teniposide, and daunorubicin); alkylating agents (e.g., melphalan, chlorambucil, busulfan, thiotepa, ifosfamide, carmustine, lomustine, semustine, streptozocin, decarbazine, methotrexate, mitomycin C, and cyclophosphamide); DNA intercalators (e.g., cisplatin, oxaliplatin, and carboplatin); DNA intercalators and free radical generators such as bleomycin; and nucleoside mimetics (e.g., 5-fluorouracil, capecitibine, gemcitabine,
  • Illustrative chemotherapeutic agents additionally include paclitaxel, docetaxel, and related analogs; vincristine, vinblastin, and related analogs; thalidomide, lenalidomide, and related analogs (e.g., CC-5013 and CC- 4047); protein tyrosine kinase inhibitors (e.g., imatinib mesylate and gefitinib); proteasome inhibitors (e.g., bortezomib); NF- ⁇ inhibitors, including inhibitors of ⁇ kinasel and other inhibitors of proteins or enzymes known to be upregulated, over-expressed or activated in cancers, the inhibition of which down regulates cell replication.
  • paclitaxel, docetaxel, and related analogs e.g., vincristine, vinblastin, and related analogs
  • thalidomide e.g., CC-5013 and CC- 4047
  • an EphA2 antibody as described herein is administered after, or at the same time, as a therapeutic agent, e.g., a chemotherapeutic agent, such as doxorubicin, that induces stress granules (“SG-inducing agent”). Increasing the amount of stress granules in cancer cells can promote targeting the tumor cells by the tumor-targeting antibody.
  • a therapeutic agent e.g., a chemotherapeutic agent, such as doxorubicin, that induces stress granules (“SG-inducing agent”).
  • exemplary therapeutic agents that can induce stress granules include pyrimidine analogs (e.g., 5-FU, under trade names of Adrucil ® , Carac ® , Efudex ® , Efudix ® ); protease inhibitors (e.g., Bortezomib, under the trade name of Velcade ® ); kinase inhibitors (e.g, Sorafenib and Imatinib, under the trade names of Nexavar ® and Gleevec ®.
  • pyrimidine analogs e.g., 5-FU, under trade names of Adrucil ® , Carac ® , Efudex ® , Efudix ®
  • protease inhibitors e.g., Bortezomib, under the trade name of Velcade ®
  • kinase inhibitors e.g, Sorafenib and Imatinib, under the trade names of Nexa
  • Arsenic compounds e.g., Arsenic trioxide, under the trade name of Trisenox ®
  • Platinum- based compounds that induce DNA damage e.g., Cisplatin and Oxaliplatin ® , under the trade names of Platinol ® and Eloxatin ® , respectively
  • agents that disrupt microtubules e.g., Vinblastin, under the trade name of Velban ® or alkabban-AQ ® ; vincristin, under the trade name of Vincasar ® , Marqibo ® , or Oncovin ®
  • Vinorelbin under the trade name of Navelbin ®
  • topoisomerase II inhibitor e.g., Etoposide, under the trade name of Etopophos, Toposar ® , VePesid ®
  • agents that induce DNA damage e.g., irradiation.
  • the tumor-targeting antibody and the SG-inducing agent is administered sequentially in any order during the entire or portions of the treatment period.
  • the tumor-targeting antibody and the SG-inducing agent is administered simultaneously or approximately simultaneously (e.g., within about 1, 5, 10, 15, 20, or 30 minutes of each other).
  • the SG-inducing agent may be administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more days before administration of the tumor- targeting antibody.
  • the SG-inducing agent is administered from 1 to 4 weeks, or longer, before the tumor-targeting antibody is administered.
  • An EphA2 antibody may also be administered to a cancer patient in conjunction with a cell- based therapy, such as natural killer (NK) cell therapy or a cancer vaccine.
  • a cancer vaccine is a peptide-based vaccine, a nucleic acid-based vaccine, a cell-based vaccine, a virus-based or viral fragment-based vaccine or an antigen presenting cell (APC) based vaccine (e.g., dendritic cell based vaccine).
  • APC antigen presenting cell
  • Cancer vaccines include Gardasil ® , Cervarix ® , sipuleucel-T (Provenge ® ), NeuVaxTM, HER-2 ICD peptide-based vaccine, HER-2/neu peptide vaccine, AdHER2/neu dendritic cell vaccine, HER-2 pulsed DC1 vaccine, Ad-sig-hMUC-l/ecdCD40L fusion protein vaccine, MVX-ONCO-1, hTERT/survivin/CMV multipeptide vaccine, E39, J65, P10s-PADRE, rV-CEA-Tricom, GVAX ® , Lucanix ® , HER2 VRP, AVX901, ONT-10, ISAlOl, ADXSl 1-001, VGX-3100, INO-9012, GSK1437173A, BPX-501, AGS-003, IDC-G305, HyperAcute ® -Renal (HAR) immunotherapy, Prevenarl3, MAGER-3.A
  • an EphA2 antibody of the present disclosure may be administered with an agent, e.g., a corticosteroid, that mitigates side-effects resulting from stimulation of the immune system.
  • an agent e.g., a corticosteroid
  • a therapeutic agent that is administered in conjunction with an EphA2 antibody of the present disclosure can be administered prior to administrations of the tumor-targeting antibody or after administration of the tumor-targeting antibody.
  • an EphA2 antibody may be administered at the same time as the additional therapeutic agent.
  • an EphA2 antibody and an additional therapeutic agent described above can be administered following the same or different dosing regimens.
  • the tumor- targeting antibody and the therapeutic agent are administered sequentially in any order during the entire treatment period or portions thereof.
  • the tumor-targeting antibody and the therapeutic agent are administered simultaneously or approximately simultaneously (e.g., within about 1, 5, 10, 15, 20, or 30 minutes of each other).
  • the therapeutic agent may be administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more days before the administration of the tumor-targeting antibody.
  • the therapeutic agent may be administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more days after the administration of the tumor-targeting antibody.
  • FUNCTIONAL ASSAYS [0335] Also described herein are functional assays that can be used to determine the ability of the antibodies described herein to mediate FcR-dependent activity.
  • the assay measures antibody dependent cellular cytotoxicity (ADCC), antibody dependent cellular phagocytosis (ADCP), or complement-dependent cytoxicity (CDC).
  • ADCC antibody dependent cellular cytotoxicity
  • ADCP antibody dependent cellular phagocytosis
  • CDC complement-dependent cytoxicity
  • the activity of the antibodies is evaluated in vivo in an animal model that is known for specific human tumors.
  • One exemplary model is the CT26 mouse model, as described in the EXAMPLES. Tumor-targeting activity of these antibodies in vivo may be assessed by using several assays, including but not limited to using flow cytometry to analyze the immune profiling of the blood and tumor, monitoring tumor growth, and performing immunofluorescence to semi-quantitative estimate tumor infiltration.
  • the effect of the antibody can be assessed using Survival, a normalized area above the curve metric (NAAC), and a normalized growth rate metric (NGRM), where NAAC and NGRM were both developed at Atreca.
  • An “in vivo active” determination can be based on the in vivo activity was assessed by a p-value ⁇ 0.05 in at least one of the analyses of survival, NAAC, and NGRM, i.e., if an antibody exhibited a p-value of less than or equal to 0.05 for survival, NAAC, and/or NGRM (any one alone being sufficient), the antibody is considered “in vivo active”.
  • antibodies that exhibit inhibitory effects on tumors including decreasing rate of tumor growth, size, tumor invasion and/or metastasis.
  • Such antibodies exhibit tumor-targeting effects in vivo, e.g., when administered to subjects that has a tumor expressing or overexpressing EphA2.
  • ENGINEERING VARIANTS [0338]
  • an antibody or variant thereof described herein is modified to have improved developability (i.e., reduced development liabilities), including but not limited to, decreased heterogeneity, increased yield, increased stability, improved net charges to improve pharmacokinetics, and or/reduced immunogenicity.
  • antibodies having improved developability can be obtained by introducing mutations to reduce or eliminate potential development liabilities.
  • antibodies having improved developability possess modifications as compared to a reference or control antibody in their amino acid sequence.
  • the antibodies or variants thereof disclosed herein have improved developability while maintaining comparable or improved binding affinity to the target antigen as compared to a reference or control (unmodified) antibody.
  • the antibodies or variants thereof disclosed herein have improved developability while maintaining activities similar to a reference or control (unmodified) antibody.
  • the antibodies or variants thereof have improved developability, e.g., as identified through various in vitro assays, such as aggregation assessment by HPLC or UPLC, hydrophobic interaction chromatography (HIC), polyspecificity assays (e.g., baculovirus particle binding), self-interaction nanoparticle spectroscopy (SINS), or mass spec analysis after incubation in an accelerated degradation condition such as high temperature, low pH, high pH, or oxidative H2O2. Mutations are successful if activity is maintained (or enhanced) while removing or reducing the severity of the liability.
  • HIC hydrophobic interaction chromatography
  • polyspecificity assays e.g., baculovirus particle binding
  • SINS self-interaction nanoparticle spectroscopy
  • mass spec analysis after incubation in an accelerated degradation condition such as high temperature, low pH, high pH, or oxidative H2O2. Mutations are successful if activity is maintained (or enhanced) while removing or reducing the severity of the liability
  • Improved properties of antibodies or variants thereof as described herein include: (1) fits a standard platform (expression, purification, formulation); (2) high yield; (3) low heterogeneity (glycosylation, chemical modification, and the like); (4) consistent manufacturability (batch-to-batch, and small-to-large scale); (5) high stability (years in liquid formulation), e.g., minimal chemical degradation, fragmentation, and aggregation; and (6) long PK (in vivo half-life), e.g., no off-target binding, no impairment of FcRn recycling, and stable.
  • Antibody liabilities are further described in Table 16. Table 16. Table 16.
  • the N-linked glycosylation site is N-X-S/T, where X is any residue other than proline.
  • This motif consists of a K or R, followed by a K or R. Stated differently, the motif can be KK, KR, RK, or RR.
  • the dipeptide NG poses a medium risk of development liability.
  • the dipeptides NA, NN, NS, and NT pose a low risk of development liability. N may also exhibit low risk of liability for other successor residues, e.g., D, H, or P.
  • dipeptide ND, NH, or NP poses a low risk of development liability.
  • dipeptide DG poses a medium risk of development liability.
  • the dipeptides DA, DD, DS, and DT pose a low risk of development liability.
  • D may also exhibit low risk of development liability for other successor residues, e.g., N, H, or P.
  • Free cysteine refers to a cysteine that does not form a disulfide bond with another cysteine and thus is left “free” as thiols. The presence of free cysteines in the antibody can be a potential development liability. Typically, an odd net number of cysteines in the protein shows a likelihood there is a free cysteine.
  • a variant was generated by introducing H76PT mutation to the heavy chain variable region of AB-009815 (SEQ ID NO: 75). This mutation removes a medium risk DP proteolytic cleavage site that could cause AB degradation during production, while in storage, or in the serum which decreases half-life after injection in mice/humans.
  • the variant retains the ADC activity of AB-009815 in tumor cells, e.g., H522, LoVo, A375, SKOV3, A549, and MDAMB231 cells (FIG. 35)
  • Another goal for engineering variants is to reduce the risk of clinical immunogenicity: the generation of anti-drug antibodies against the therapeutic antibody.
  • the antibody sequences are evaluated to identify residues that can be engineered to increase similarity to the intended population’s native immunoglobulin variable region sequences.
  • the factors that drive clinical immunogenicity can be classified into two groups. First are factors that are intrinsic to the drug, such as: sequence; post-translational modifications; aggregates; degradation products; and contaminants. Second are factors related to how the drug is used, such as: dose level; dose frequency; route of administration; patient immune status; and patient HLA type. [0345]
  • One approach to engineering a variant to be as much like self as possible is to identify a close germline sequence and mutate as many mismatched positions (also known as “germline deviations”) to the germline residue type as possible.
  • Germline gene IGHD codes for part of the H-CDR3 region but typically exhibits too much variation in how it is recombined with IGHV and IGHJ (e.g., forward or reverse orientation, any of three translation frames, and 5’ and 3’ modifications and non-templated additions) to present a “self” sequence template from a population perspective.
  • Each germline gene can present as different alleles in the population.
  • the least immunogenic drug candidate in terms of minimizing the percent of patients with an immunogenic response, would likely be one which matches an allele commonly found in the patient population.
  • Single nucleotide polymorphism (SNP) data from the human genome can be used to approximate the frequency of alleles in the population.
  • SNP single nucleotide polymorphism
  • Another approach to engineering a lead for reduced immunogenicity risk is to use in silico predictions of immunogenicity, such as the prediction of T cell epitopes, or use in vitro assays of immunogenicity, such as ex vivo human T cell activation. For example, services such as those offered by Lonza, United Kingdom, are available that employ platforms for prediction of HLA binding and in vitro assessment to further identify potential epitopes.
  • Antibody variants can be designed to enhance the efficacy of the antibody.
  • design parameters can focus on CDRs, e.g., CDR3. Positions to be mutated can be identified based on structural analysis of antibody-antigen co-crystals (Oyen et al., Proc. Natl. Acad Sci. USA 114: E10438-E10445, 2017; Epub Nov 14, 2017) and based on sequence information of other antibodies from the same lineage.
  • Approaches to mutation design [0349] Development liabilities can be removed or reduced by one or more mutations. Mutations are designed to preserve antibody structure and function while removing or reducing development liabilities and to improve function.
  • mutations to chemically similar residues can be identified that maintain size, shape, charge, and/or polarity. Illustrative mutations are described in Table 17. Table 17. Preferred mutations to remove development liabilities i Odd # C i h METHODS FOR ALTERING THE GLYCOSYLATION OF AN ANTIBODY [0350]
  • the antibodies described herein comprise an Fc region having altered glycosylation that increase the ability of the antibody to recruit NK cells and/or increase ADCC.
  • the Fc region comprises glycan containing no fucose (i.e., the Fc region is afucosylated).
  • Fucosylated antibodies can be produced using cell lines that express a heterologous enzyme that depletes the fucose pool inside the cell (e.g., GlymaxX ® by ProBioGen AG, Berlin, Germany). Non-fucosylated antibodies can also be produced using a host cell line in which the endogenous ⁇ -1,6-fucosyltransferase (FUT8) gene is deleted. See Satoh, M. et al., “Non-fucosylated therapeutic antibodies as next-generation therapeutic antibodies,” Expert Opinion on Biological Therapy, 6:11, 1161-1173, DOI: 10.1517/14712598.6.11.1161.
  • the EphA2 antibodies disclosed herein can also be used for diagnosing a patient having a cancer suitable for treatment.
  • the method comprises contacting a tumor sample from the patient with an antibody disclosed above and detecting binding of the antibody to the tumor sample.
  • the antibodies are conjugated to a detectable label that produces fluorescent, luminescent or colorimetric signals, and detecting the signal from the label indicates that tumor is suitable for treatment with an EphA2 antibody disclosed herein.
  • a labeled secondary antibody is added to the tumor sample that have been contacted with the antibody disclosed herein and detecting the signal from the secondary antibody indicates that the tumor expressing or overexpressing EphA2.
  • an EphA2 antibody may display donor-specific tumor selectivity, i.e., the antibody may show tumor selectivity in some donors but not other donors. In these cases, it is desirable to determine the binding of the tumor to the EphA2 antibody before treating the patient.
  • SCREENING ANTIBODIES Also disclosed herein is a method for selecting a tumor-targeting antibody.
  • the method comprises contacting an antibody disclosed above with a polypeptide comprising SEQ ID NO: 94 or SEQ ID NO: 95 and contacting the antibody with a tumor cell and selecting the antibody if the antibody binds to the polypeptide and binds preferentially to the tumor cell as compared to normal cell.
  • AB-008873 was discovered in antibody repertoires generated by Immune Repertoire Capture® (IRCTM) technology from plasmablast B cells isolated a non-small cell lung cancer patient with an active anti-tumor immune response after treatment with the anti-PD-1 antibody OPDIVO® (nivolumab) (Bristol Myers Squibb). AB-008873 was tested for cell surface binding to 6,000 human membrane proteins expressed on the surface of HEK293 cells by flow cytometry. Two membrane proteins showed binding over the background: EphA2 and FcGR1. No other ephrin type-A or type-B receptors had a binding signal above the background.
  • IRCTM Immune Repertoire Capture®
  • AB-008873 was further shown to bind the extracellular domain of EphA2 via an indirect and reverse indirect ELISA. The ELISAs also confirmed binding to mouse EphA2. [0357] Next, AB-008873 was tested to determine if the previously observed the in vitro surface binding to A549 of the antibody was mediated by interaction with EphA2.3 EphA2 guide RNAs were introduced into Cas9 overexpressing A549 cells. The EphA2 guide RNAs were designed by Synthego and Chop CRISPR tool. Exact sequences were selected based on low off-target score. The designed sgRNAs were synthesized and modified by Synthego.
  • Electroporations of guide RNA was performed using the NeonTM Transfection System 10 ⁇ L Kit #MPK1096 according to the manufacturer’s protocol. Final concentrations of the sgRNA were 100 ⁇ M (100 pmol/ ⁇ l). This resulted in a knockout of EphA2 gene in >90% of cells.
  • the polyclonal EphA2 KO A549 cell population was then cultured for ⁇ 4 days and assayed for cell surface binding by AB-008873. The fraction of cells in the AB-008873 positive gate was reduced from ⁇ 98% (irrelevant guide RNA) to ⁇ 10%, thus confirming EphA2 is the primary driver of AB-008873 A549 binding.
  • EXAMPLE 2 EXAMPLE 2.
  • AB-008873 VARIANTS [0358] The sequence of AB-008873 was analyzed for potential liabilities. There are no high-risk liabilities. There is a medium-risk proteolytic cleavage site at H75D-H76P (i.e., heavy chain position 75 aspartate followed by heavy chain position 76 proline) and a medium-risk deamidation site at H108N-H109G.
  • Low-risk liabilities include tryptophan oxidation at H34W and L90W; asparagine deamidation at H60N-H61N and L25N-L26N; lysine glycation at H67K, H100K, and L30K; and aspartate isomerization at H115D-H116A, L49D-L50D, L50D-L51S, and L91D-L92S.
  • AB-008873 was aligned to its closest human germline genes (IGHV4-34*02, IGHD2-8*01, IGHJ3*02, IGLV3-21*02, and IGLJ2*01), and to four of its known siblings (AB-009805, AB-009806, AB-009807, and AB-009808). Three variants were designed to explore differences between AB- 008873 and its siblings.
  • AB-009812 was designed with mutation H54RS to AB-008873 (heavy chain position 54 mutated from arginine to serine), to match H54S as found in the siblings and germline, and to create the N-linked glycosylation motif found in the siblings and germline (H52N-H53H-H54S).
  • AB- 009813 was designed with mutation H54RA to AB-008873, to remove the H54 arginine from AB- 008873, but not create an N-linked glycosylation motif (ie, H52N-H53H-H54A is not an N-linked glycosylation motif).
  • AB-009814 was designed with deletion of three residues, H61N-H62Y-H63N, to match the siblings and germline in that region. Note that AB-009814 could equivalently be described as a deletion of H60N-H61N-H62Y, H59Y-H60N-H61N, or H58N-H59Y-H60N and the resulting sequence is the same. [0360] AB-009815 and AB-009816 were designed to remove the medium-risk proteolytic cleavage liability in AB-008873 at H75D-H76P. The variants make the mutation H76PT or H76PA, respectively. AB-009815 with the H76PT mutation also changes the sequence o germline.
  • AB-009817 was designed to remove the medium-risk deamidation site at H108N-H109G.
  • the variant makes the mutation H109GA relative to AB-008873, to reduce the liability to a low risk deamidation site (i.e., NG is medium risk, but NA is low risk).
  • H106C and H111C are predicted to form an intra-H3 disulfide bond, with H107-H110 in a 4-residue turn.
  • Alternative approaches to removing the medium risk deamidation site include H108NS, H108NA, H108NQ, H108NL, or H108NY.
  • AB-008873 siblings AB-009805, AB-009806, AB-009807, AB-009808, and variants AB- 009812, AB-009813, AB-009814, AB-009815, AB-009816, and AB-009817 were synthesized on a mouse IgG2a framework. All siblings show less binding, less ADCC, and less ADCP activity than AB- 008873. See, FIG. 20.
  • Variants AB-009815 and AB-009816, which remove the same medium-risk cleavage site, show similar levels of binding and activity as AB-008873.
  • AB-009817 completely loses binding (tested up to 1 ⁇ M) and functional activity (tested up to 100 nM).
  • Variants AB-009812, AB- 009813, and AB-009814 show some binding and ADCC activity, though less than AB-008873. These results show that the N-linked glycosylation motif and the 3-aa insertion in H2 region affect binding, but they are not essential.
  • the ADC (antibody-drug conjugate) activity of AB-009815 is the same as that of AB-008873. See, FIG.21A-C and Table 18. Table 18.
  • AB-010146 makes H129AS.
  • AB-010147 makes L60QR.
  • AB-010148 combines H51VI and H86TS.
  • AB-010149 combines H51VI and H129AS.
  • AB-010150 combines H86TS and H129AS.
  • AB-010151 combines H51VI, H86TS, and H129AS.
  • AB-010152 combines H51VI, H86TS, H129AS, and L60QR. Further combinations of mutations to germline are of interest.
  • Anti-EphA2 Variants AB-010141, AB-010142, AB-010143, AB-010144, AB-010145, AB- 010146, AB-010147, AB-010148, AB-010149, AB-010150, AB-010151, and AB-010152 were synthesized on a mouse IgG2a framework and assayed for ADCC, both by EC 50 and delta-activity as compared AB-008873 and melting temperature (Tm) measured using UNcle instrument. The results of these assays are shown in Table 19. Table 19. Properties of anti-EphA2 antibodies
  • AB-010141 with the H31DG mutation exhibits improved ADCC EC 50 but decreases Tm by approximately 1 o C.
  • AB-010143 with L97LV exhibits improved Tm by approximately 1 o C.
  • AB-010147 with L60QR exhibits improved Tm by approximately 2 o C but might exhibit somewhat decreased ADCC activity.
  • AB-010148 with H51VI and H86TS exhibits similar Tm and ADCC activity as compared to AB-008873.
  • AB-010148 was selected based on Tm and ADCC activity similar to that of AB-008873, while incorporating H76PT to remove the medium-risk DP proteolytic cleavage site and incorporating H51VI and H86TS to remove germline deviations to reduce potential immunogenicity.
  • Combinations of L31DG, L97LV, and/or L60QR were added to AB-010148 to improve Tm, improve ADCC activity, and/or remove germline deviations.
  • H31DG is predicted to remove an intramolecular salt bridge between H31D and H54R.
  • H31DG was combined with either H54RA or H54RQ, along with L97LV and optionally L60QR, in variants AB-010364, AB- 010365, AB-010366, and AB-010367.
  • Antibody variants AB-010357 – AB-010367 were synthesized on a mouse IgG2a framework and assayed for ADCC, both by EC 50 and delta-activity (i.e., change in activity) as compared AB- 008873 and melting temperature (Tm) measured using UNcle instrument. The results of these assays are shown in Table 20. Table 20. Properties of Anti-EphA2 antibodies
  • Antibodies AB-010357, AB-010361, and AB-010363 were then used as the basis for generation of further variants.
  • AB-010357 was mutated to generate AB-010661, AB-010662, AB- 010663, AB-010664, AB-010665, AB-010666, AB-010667, AB-010668, AB-010669, AB-010670, AB-010671, AB-010672, AB-010673, and AB-010674.
  • AB-010361 was mutated to generate AB-010675, AB-010676, AB-010677, AB-010678, AB-010679, AB-010680, AB-010681, AB-010682, AB-010683, AB-010684, AB-010685, AB- 010686, AB-010687, and AB-010688.
  • AB-010363 was mutated to generate AB-010689, AB-010690, AB-010691, AB-010692, AB-010693, AB-010694, AB-010695, AB-010696, AB-010697, AB-010698, AB-010699, AB- 010700, AB-010701, and AB-010702.
  • EXAMPLE 3 IN VITRO STUDIES Immunophenotyping [0373] Peripheral blood was blocked with 1:100 TruStain FcX PLUS Antibody (BioLegend 156604) for 10min at 4 o C and stained for 30 min at 4 o C with a mastermix of antibodies for each panel.
  • Tumors were digested using Miltenyi’s gentleMACS Octo Dissociator with heaters and Tumor Dissociation Kit, mouse (130-096-730), according to the manufacturer’s instructions.
  • the dissociated cells were cryopreserved in 10%FBS/DMSO.
  • Dissociated cells were thawed using pre- warmed 2%FBS/RPMI dropwise, centrifuged at 300xg for 10 min, with supernatant decanted. Cells are blocked TruStain FcX PLUS Antibody (BioLegend 156604) for 10min at 4 o C and stained with a mastermix of antibodies for 30 min at 4 o C.
  • Tumors treated with AB-008873 showed no significant changes in the percentage of tumor infiltrating leukocytes (TILs) by flow cytometer at days 10 and 17 post inoculation compared to PBS treated controls. FIG.10. Similarly, no significant changes in T cells, NK cells, monocytes/M-MDSCs, granulocytes/G-MDSCs were detected in the tumor at days 10 and 17 (FIG. 11 and FIG. 18) while total macrophages were increased at day 10 in mice treated with 40mg/kg AB-008873. Tumors collected at endpoint and treated with 40mg/kg AB-008873 showed evidence of decreased TILs, M- MDSCs, and slight increases in cDC1.
  • TILs tumor infiltrating leukocytes
  • FIG.12 and FIG.17 Binding Assays Flow Screen (in vitro) Method: [0377] Surface binding of the antibodies to in vitro grown cell lines was assessed by flow cytometry. Tumor cells were detached from their culture plate using Versene and counted. Cells were staining in BSA-containing buffer with primary antibody for 30 minutes at 4 ° C with shaking. Following, cells were washed and stained with secondary PE-labeled antibody for 30 minutes at 4°C with shaking. Before analysis on an Intellicyt iQue3 scanner, cells were counterstained with DAPI. MedFI values from live, single cells was expressed as fold over isotype control.
  • AB-008873 was conjugated using Thermo’s SiteClickTM R-PE Antibody Labeling Kit for testing on dissociated CT26 ex vivo cells. Dissociated cells were thawed and cells were blocked with TruStain FcXTM (anti-mouse CD16/32) Antibody and stained with PE-conjugated antibodies and CD45-BV605 for 30 min at 4°C. Cells were washed 3 times with 200 ⁇ l 1%FBS/1mM EDTA/PBS and resuspended in assay buffer containing DAPI. Cells were analyzed using the Cytoflex and FlowJo_v10.7.1.
  • AB-008873 Surface binding of AB-008873 on several in vitro mouse and human tumor cell lines was assessed using flow cytometry. Among the cell lines screened, AB-008873 show binding on 786-O, A375, A549, H522, LoVo, MDA-MB-231, PC3, RKO, SKOV3, SW1116, and CT26. Additionally, AB-008873 bound CT26 ex vivo cells.
  • FIG.1 Tables 23 and 24. Table 23. Surface binding profile of AB-008873 in human cell lines Table 24.
  • ADCC Antibody-dependent cellular cytotoxicity
  • ADCC activity of AB-008873 was assessed on several in vitro human and mouse tumor cell lines. Among the cell lines screened, AB-008873 showed dose-dependent ADCC on A549, MDA-MB- 231, CT26, and to a small extent, on EMT6 cells. AB-008873 did not show any ADCC when the antibody was used up to 100 nM on SKBR3. FIG.2A-2B and Table 25.
  • AB-009806 showed the best binding and functional activity, followed by AB-009805.
  • AB-009807 and AB-009808 showed little binding and ADCC activity but some ADCP activity.
  • FIG.20 Engineered variant antibodies of AB-0008873 were tested for binding and for ADCC activity on A549 tumor cells. Compared with AB-008873, AB-009815 and AB-009816 showed similar levels of binding and ADCC activity as AB-008873.
  • AB-009812 and AB-009813 showed weaker binding and ADCC activity, followed by AB-009814.
  • AB-009817 did not show any substantial binding or ADCC activity on A549 up to 100 nM.
  • FIG.21. [0384] AB-010357, AB-010361, and AB-010363 and variants (Table 27) based on those antibodies exhibited ADCC activity greater than AB-008873 on the A549 tumor cells. All the variants tested exhibited ADCC activity at least as good as their parental antibody. Several variants showed a 10-to- 100-fold increase in potency as compared to their parent, with some variants showed a greater than 700- fold increase.
  • AB-010685, AB-010671, and AB-010699 had EC50 values under these assay conditions of approximately 6 pM.
  • AB-010681 and AB-010695 had EC 50 values of approximately 8 pM and 10 pM, respectively.
  • FIG. 40 and Table 26 It is notable that both AB-010685 and AB-010699 have the same double mutations L29SY and L92SH. See Table 28.
  • AB-010699 and AB-010361 exhibited greater ADCC activity on A549 cells than AB- 010018, while both AB-010699 and AB-010695 were more toxic than cetuximab on A549 cells.
  • FIG. 50A and 50B AB-010699 showed several thousand-fold higher ADCC activity on A549 cells and higher thermostability (as reflected in a 2.0oC higher Tm1) as compared to AB-008873.
  • AB-010685 was also highly potent on PC3-KILR cells and exhibited a 10-fold improvement in ADCC as compared to AB-010018.
  • FIG.52 shows
  • ADCP antibody-dependent cellular phagocytosis
  • the cell membranes of target cells were labeled with green fluorescent membrane dye preceding opsonization with different concentrations of antibody at room temperature for 30 minutes.
  • RAW264.7 mouse macrophage (effector) cells were then added at a 1:1 ratio with the target cells and co-cultured at 37 ⁇ C and 5% CO 2 for 2 hours. After incubation, the cell mixture was dissociated with 2 mM ethylenediaminetetraacetic acid (EDTA, pH 7.4). The cell suspension was then washed several times in an isotonic salt solution and probed with a commercially available anti-CD11b antibody, conjugated with Allophycocyanin (APC).
  • EDTA ethylenediaminetetraacetic acid
  • ADC [0389] AB-008873 was tested for its antibody-drug conjugate activity using a secondary, toxin- conjugated antibody.
  • target cells were detached from the culture plate and cell concentration was adjusted to 31,250 cells/mL in assay media.
  • 2,500 cells were added to each well of a 96 well plate and incubated with different concentrations of primary antibody for 15 min at room temperature.
  • secondary Fab anti-mouse IgG Fc conjugated to Duocarmycin with a cleavable linker (Moradec, #AM-202-DD) was added at a final concentration of 250 ng/mL. Cells were incubated for 72h at 37 ⁇ C and 5% CO 2 .
  • AB-008873 was assessed on several in vitro human and mouse tumor cell lines. Among the cell lines screened, AB-008873 showed dose dependent ADC on A549, SKOV3, MDA-MB-231, A375, LoVo, H522, RKO, and PC3. As shown in FIG.3, AB-008873 demonstrated ADC activity on these tumor cells.
  • the ADC activity of AB-008873 was compared to the engineered variant AB-009815 (H76PT mutation) on H522, LoVo, A375, SKOV3, A549, and MDA-MB-231 cells.
  • AB-009815 showed similar activity compared to AB-008873 in all cell lines tested. As shown in FIG.35 show that the ADC activity of AB-009815 is substantially identical to AB-008873 on these tumor cells.
  • the ADC activity of AB-010361 and AB-010699 was assayed as described above and was compared to that of AB-008873, with the results shown in FIG.51.
  • Both AB-010361 and AB-010699 had similar ADC activity as AB-008873 in cells expressing high levels of EphA2 and exhibited enhanced ADC activity in cells expressing low levels of EphA2.
  • Thermostability [0393] AB-010357, AB-010361, and AB-010363 and variants based on those antibodies were assayed for thermostability using an Unchained Labs UNcle instrument. The concentration of purified antibodies was adjusted as needed to between 0.2 mg/ml and 0.5 mg/ml in PBS immediately prior to analysis.
  • Tm melting temperature
  • Mouse CT26 tumor cells were propagated in culture by passaging cells every 2 to 3 days (1:10 subcultures) for 6 passages. On the day of inoculation, cells were collected, counted, and diluted to 5 ⁇ 10 6 cells/mL in RPMI medium without supplements. Cell viability was recorded as 86.8% at time of inoculation.
  • Female, 6-week-old BALB/c mice were inoculated in the right hind flank by subcutaneous injection with 1 ⁇ 10 6 CT26 cells/mouse in 0.2 mL Waymouth’s media without supplements. The day of cell inoculation was designated as Study Day 0.
  • mice were inoculated with CT26 tumor cells on Study Day 0. To achieve study groups with consistent and homogenous tumor volumes an overage of approximately 50% was included. Mouse tumors routinely became visible and palpable five days after cell inoculation. Tumor volumes were measured twice prior to randomization. On Study Day 9, mice were randomized to ensure homogenous tumor volumes using the ‘matched distribution’ randomization function of the StudyLog lab animal management software. Mice with pre-ulcerated tumors, irregular shaped tumors, or multiple tumors were excluded from randomization. Animal IDs were assigned randomly within each treatment group on the day of randomization.
  • Test article AB-008873 was administered starting on Day 8 by intraperitoneal (IP) injection twice weekly at 20 or 40 mg/kg based on group mean body weight. Mice received either 1 or 3 doses before they were removed from study for analysis two days after dosing (Day 10 or Day 17, respectively). [0398] Mice in the vehicle control groups were dosed at 10 mL/kg DPBS based on group mean body weight using the same dosing schedule as the test article. Termination [0399] Mice were euthanized by (1) carbon dioxide asphyxiation followed by cervical dislocation or (2) isoflurane inhalation and cardiac puncture followed by cervical dislocation at predetermined time points (i.e., Day 10 or Day 17).
  • Blocks containing tumors were sectioned at 5 ⁇ m using a Accu-Cut ® SRMTM 200 Rotary Microtome (Sakura). Sections were mounted to slide and dried. In one exemplary procedure, samples (e.g., tumor samples) were sectioned by longitudinal slicing into 2 or 3 mm thick slices using a mold. Sections are then embedded face down for examination. This approach is ideal for assessing infiltrates across the tumor and fitting multiple tumors per block.
  • FIG. 7 and Table 30 show the procedures and reagents used in an in vivo study to assess the effect of the AB-008873 treatment to mice. Table 30.
  • Immunofluorescence staining was performed on 5 ⁇ m formalin-fixed paraffin-embedded tissue sections of mouse CT26 tumors following standard immunostaining protocols. The primary antibodies were utilized with species-specific secondary antibodies and detected using standard methodology. [0404] The tissue sections were baked at 65°C for 30 minutes, dewaxed in xylene and rehydrated. Antigen retrieval was performed under high pressure either at 95°C for 20 minutes or 110°C for 15 minutes using Target Retrieval Solution (Dako) in Decloaking Chamber NxGen (Biocare Medical). The sections were blocked for 15 minutes at room temperature with Bloxall (Vector Labs).
  • Target Retrieval Solution Dako
  • Decloaking Chamber NxGen Biocare Medical
  • T Cell Marker Protocol Dual labeling for cytotoxic T cells (“T cyt cells”, which are CD3+CD8+) and regulatory T cells (T reg cells, i.e., CD4+/forkhead-box protein P3; FoxP3+) populations was performed as follows. Following antigen retrieval and blocking with Bloxall, tissue sections were blocked in blocking buffer (3% bovine serum albumin with 3% normal donkey serum in 1X phosphate-buffered saline) for 30 minutes or 1 hour at room temperature. After blocking, the slides were incubated with primary antibodies against CD8 for 1 hour at room temperature, FoxP3 overnight at 4°C, or with species- appropriate isotype controls at corresponding times and temperatures.
  • blocking buffer 3% bovine serum albumin with 3% normal donkey serum in 1X phosphate-buffered saline
  • DC cells i.e., CD3- CD103+
  • tissue sections were blocked in blocking buffer (3% bovine serum albumin with 3% normal donkey serum in 1X phosphate-buffered saline) for 30 minutes or 1 hour at room temperature. After blocking, the slides were incubated with the primary antibody against CD103 for 1 hour at room temperature or with the species-appropriate isotype control at corresponding time and temperature.
  • blocking buffer 3% bovine serum albumin with 3% normal donkey serum in 1X phosphate-buffered saline
  • Macrophage Marker Protocol Following antigen retrieval and blocking with Bloxall, tissue sections were successively blocked for 15 minutes with Avidin block (Biocare), Biotin block (Biocare), and blocking buffer (3% bovine serum albumin with 3% normal donkey serum in 1X PBS) for 1 hour at room temperature. After blocking, the slides were incubated with primary antibodies against F4/80 and inducible nitric oxide synthase (iNOS), F4/80 and Arginase-1 (Arg-1), or species-appropriate isotype controls overnight at 4°C.
  • iNOS inducible nitric oxide synthase
  • Arg-1 Arginase-1
  • Table 31 Marker Phenotype for Immune Cell Subsets Results
  • a significant increase in CD3+ and CD4+ cell populations with a concomitant decrease in Treg cells was observed in CT26 tumors from mice treated with 40 mg/kg AB-008873 vs PBS by 10 days after administration of the antibody.
  • FIGs.13-15 By Day 17, a significant increase in cytotoxic T cells and M1 macrophages (i.e., pro-inflammatory macrophages) were noted in CT26 tumors from mice treated with AB-008873 vs. PBS.
  • the results are summarized in Tables 32 and 33.
  • AB-008873 did not demonstrate significant anti-tumor activity vs PBS at either 20 mg/kg or 40 mg/kg.
  • FIG.23 depicts binding sites of commercial anti-EphA2 antibodies.
  • commercial anti-EphA2 antibodies bind to the extracellular domain or intracellular domain of Eph2A.
  • MAB3035 (a.a.
  • LS-C36249-100 extracellular domain
  • LS-C100255-400 a.a. 30-60
  • LS-B1794-50 a.a. 450-500
  • Ab73254 extracellular domain
  • 6997S around a.a. Arg907
  • NSCLC non-small cell lung cancer
  • NSCLC-adenocarcinoma i.e., clear cell and papillary subtypes
  • melanoma esophageal cancer
  • breast cancer i.e., triple negative, hormone receptor-positive, and HER2-positive molecular phenotypes
  • colorectal cancer soft tissue sarcoma
  • pancreatic, prostate and urotheli
  • Antibodies tested on human tumor and tumor adjacent tissues in immunofluorescence studies [0416] In brief, commercially obtained frozen resected tumor samples and tumor adjacent tissue from non-autologous patients were sectioned to slide and lightly fixed using 4% paraformaldehyde. Following a buffer wash, the slides were incubated in a blocking reagent containing 2.5% normal donkey serum in phosphate-buffered saline (PBS), pH 7.0, at room temperature and then incubated overnight at 4°C in primary antibody diluted in 2.5% donkey serum in PBS (concentration range of 0.1 – 30 ug/mL).
  • PBS phosphate-buffered saline
  • the primary antibody is a chimeric sequence comprised of a human Fv derived from the Atreca library and a mouse IgG2a Fc sequence. After the primary antibody and subsequent wash in buffer solution, the slide is incubated in donkey anti-mouse secondary antibody conjugated to AlexaFluor 647 at room temperature. Following a wash step, the tissue is counterstained with Hoescht dye which ubiquitously labels cell nuclei, washed again, and coverslipped.
  • AB-008873 immunoreactivity was detected in NSCLC adenocarcinoma, melanoma, esophageal cancer, ovarian cancer, HER2+ breast cancer, soft tissue sarcoma, anal cancer, gastric cancer, uterine cancer, and head and neck cancer.
  • FIGs.25-27. AB-008873 showed approximately 80% overlap of immunoreactive tumor cores with the AB-010018 and 90% with the commercial antibody derived against the EphA2 extracellular domain. Table 35.
  • AB-008873 and its engineered variants demonstrated a punctate binding pattern across multiple cancer types including ovarian and uterine cancers and soft tissue sarcoma while any labeling by antibodies AB-010018, AB- 010016, and AB-010017 or commercial antibodies was diffused with cytoplasmic signal predominant.
  • FIGs.26-28 Table 35. IHC score of AB-008873 and its variants on 21 types of fresh frozen human tumor and TAT
  • AB-010361 and AB-010363 were assayed as above. Both variants retained similar reactivity as AB-008873 to most of the tested cancer samples. However, there were some notable differences observed for reactivity to melanoma, soft tissue sarcoma, endometrioid uterine cancer, esophageal cancer, triple negative breast cancer, ovarian cancer, and urothelial cancer.
  • AB-010361 and AB-010363 show higher binding affinity than AB-008873 on melanoma, soft tissue sarcoma, endometrioid uterine cancer.
  • AB-010361 shows higher binding affinity than AB-008873 on esophageal cancer and triple negative breast cancer.
  • AB-010363 shows higher binding affinity than AB-008873 on ovarian cancer, and urothelial cancer.
  • AB-010361 shows enhanced reactivity in triple negative breast cancer as compared to AB-010363, but diminished reactivity as compared to AB-010363 in ovarian and urologic cancer.
  • AB-010363 shows enhanced reactivity in urothelial cancer compared to AB- 010361, AB-010018, AB-010016, and AB-010017, but diminished tumor-selective binding in esophageal cancer as compared to AB-008873.
  • Table 36 illustrates reactivity of anti-EphA2 antibodies to cancers. Table 36. Reactivity of anti-EphA2 antibodies to cancers ll Table 36 (Continued) Score of 1 indicates no signal above TAT or isotype control. [0419] AB-010699 showed increased potency in many tumor types as compared to AB-010018 and AB-00873 and AB-010361.
  • FIG.42 Table 37, 38, and 39.
  • Table 37 Binding to EphA2 epitopes across cancer types by various EphA2 antibodies Score of 1 indicates no signal above TAT or isotype control.
  • Table 38 Binding to EphA2 epitopes across cancer types by various EphA2 antibodies
  • AB-010016 and AB- 010017 that bind to the ligand binding domain of EphA2 and AB-010018 were tested for reactivity over the same set of tissue samples as AB-010699, all at a concentration of 3 ug/ml. As shown in FIG. 24, the signal of these three comparator antibodies was very low for many of the samples tested. The assay was repeated with increased concentrations, with AB-010016 and AB-010017 being tested at 30 ug/ml and AB-010018 being tested at 10 ug/ml while AB-010699 was maintained at 3 ug/ml. AB- 010699 showed a differentiated reactivity over all three comparator antibodies tested. FIG.31.
  • the slides were incubated with AB-008873, its engineered variants, antibody AB-010018, or mouse IgG2a, the isotype control, at 3 ⁇ g/mL, overnight at 4 ⁇ C.
  • Commercial antibodies were also tested at 10 ⁇ g/mL.
  • the slides were washed with Wash Buffer and incubated with a secondary for 40 minutes at room temperature.
  • the slides were washed and then the chromogenic reaction was developed by incubating them in Betazoid DAB for 2 minutes. After the color development the slides were counter stained with Hematoxylin QS for 15 seconds, dehydrated, mounted and then imaged in AxioScan whole slide scanner.
  • Antibodies being tested include AB-008873 and engineered variants include AB-009812, AB-009813, AB-009815, AB-009816, AB-010018, and commercial anti-Eph2A antibody (LC-C100255-400, LS-B174-50).
  • Table 40 Unlike AB-008873, the antibody AB-010018 revealed enhanced labeling of epithelium in stomach as well as moderate signal with renal tubules. Similar normal tissue staining profiles were noted with the commercial antibodies tested.
  • FIG. 43A EXAMPLE 6.
  • EPITOPE BINNING BY BIO-LAYER INTERFEROMETRY [0426] Epitope binning was performed using an Octet Red 96E instrument (Sartorius) using the in- tandem format. In this format, antigen is captured on a biosensor tip, a first antibody (or other binding partner) is bound to saturation, and subsequently the ability of a second antibody (or binding partner) known to recognize the antigen is assessed.
  • the Fv regions for three of the antibodies were derived from therapeutic candidates that entered human clinical trials: AB-010016 derived from MedImmune’s MEDI-547, disclosed in Peng et al., J. Mol. Biol. 2011 Oct. 21; 413(2): 390-405. doi: 10.1016/j.jmb.2011.08.018; AB-010017 derived from Merrimack’s MM-310, disclosed in Geddie et al., MAbs. 2017 Jan; 9(1): 58-67. Doi: 10.1080/19420862.2016.125904; Kamoun et al., Nat Biomed Eng. 2019 Apr;3(4):264-280. doi: 10.1038/s41551-019-0385-4.
  • the fourth antibody Fv region was discovered via Atreca’s Immune Repertoire Capture (IRC TM ).
  • Antibodies were produced with mouse IgG2a constant regions.
  • the natural ligand tested was EphrinA1 fused to Fc (Acro, EF1-H5251).
  • Antigen immobilized on the biosensor was the extracellular domain of human EphA2 (25-534) with a C-terminal HIS tag (R&D Systens, 3035-A2) and captured using Ni-NTA tips (Sartorius, 18-5102).
  • Protein solutions were made in 1X Kinetics buffer (Satorius, 18-1092) supplemented with 2.5 mM Imidazole to reduce non-specific binding.
  • the first bin contains molecules AB-008873 and AB-010018 and was interpreted to represent epitopes on the membrane proximal fibronectin domain of EphA2 based on the reported epitope location of DS-8895a (Hasegawa, J. et al., Novel anti-EPHA2 antibody, DS- 8895a for cancer treatment. Cancer Biology and Therapy, 17(11), 1158–1167 (2016)).
  • the second bin contains molecules AB-010017, AB-010016, and EphrinA1-Fc and was interpreted to represent epitopes on the ligand binding domain (Peng, L. et al., Structural and functional characterization of an agonistic anti-human EphA2 monoclonal antibody. Journal of Molecular Biology, 413(2), 390–405 (2011); Geddie, M. L. et al., Improving the developability of an anti-EphA2 single-chain variable fragment for nanoparticle targeting. MAbs, 9(1), 58–67 (2017)). FIG. 5, Tables 41-42.
  • the FN2 location in the first bin is inferred from domain deletion data reported in Hasegawa et al., 2016, FIG.1, noting that the reported MMP cleavage sites are (385/395/432/435).
  • Table 41 Results of Octet in tandem binning for epitope mapping Table 42.
  • Epitope recognized by AB-008873 overlaps with that of AB-010018 Epitope Domain Investigation by Yeast Surface Display [0429]
  • subdomains of human EphA2 and chimeras of human EphA2 and human EphA4 were displayed on the surface of yeast.
  • AB-008873 had shown binding to EphA2 but not homologous receptor EphA4 in other assays (screening at Integral Molecular). 5 constructs (shown in Table 43) were selected for display on the surface of yeast and staining via AB-008873: Table 43. EphA2 subdomains [0430] Constructs were expressed as Aga2 fusions with an internal HA tag between Aga2 and the displayed protein as well as a C-terminal Myc tag (Boder, E. T., & Wittrup, K. D., Yeast surface display for screening combinatorial polypeptide libraries. Nature Biotechnology, 15(6), 553–557 (1997)).
  • Yeast cells were cultured in SDCAA (Teknova, S0543) and induced with SGCAA (Teknova, S0542). Cells were stained with pairs of primary and secondary antibodies.
  • AB-008873 Lot 2 (Atum, mIgG2a) and Donkey anti-Mouse IgG AF647 (JacksonImmunoResearch 715-605-150) were used for 10-point titrations to assess 8873 binding.
  • Chicken IgY anti-cMyc Life technologies A21281
  • Goat anti Chicken IgY FITC (Life technologies A11039) were used to assess expression levels. The analysis was run on the iQue3 flow cytometer.
  • EphA4 chimeras offer stability advantages and can inform the finer mapping at the domain-level by expressing EphA2 nestations.
  • FN2 domain (EphA2-FN2) alone shows strong binding signal (triangle).
  • FN2 domain alone also has high relative expression.
  • EphA2 full ECD shows a binding signal (circle) relatively lower than the binding signal driven by the FN2 domain alone.
  • EphA4 full ECD shows no binding signal (square). Swapping the FN1 domain from EphA4 into EphA2 enables binding of the epitope (diamond). Binding is lost when the FN2 domain from EphA4 is swapped into EphA2.
  • FIG.45 However, the epitope residues are conserved across species commonly used in toxicology studies.
  • FIG. 46 The epitope of AB-008873 is located on the opposite side of the FN2 domain from the reported LBD-FN2 site. See Nikolov, D. B et. al. (2014) Cell Adh Migr 8, 360-365. [0432] Co-crystallization studies showed that the disulfide loop in the HCDR3 of AB-008873 demonstrated substantial rotation as compared to the structure without target interaction.
  • FIG. 47 Furthermore, the co-crystal and yeast display data aligned and provided additional details on the epitope.
  • AB-010018 was shown to bind to Thr472, Arg474, Asp478, Ser479, Asn480, Gly477, and Leu504 in this assay.
  • EXAMPLE 7. BINDING AFFINITY Steady State KD [0434] Binding of antibodies to the FN2 domain of hEphA2 was measured using the Biacore ® T200 SPR system at 25°C using HBS-EP+ buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% v/v Surfactant P20).
  • Antibodies in mIgG2a format were captured at levels between 475-715 RU via an anti-mouse Fc antibody immobilized to a CM5 chip. Binding was assessed using a titration of C-terminally His-tagged hEphA2-FN2 (Thr437-Asn534 + His tag) associated for 30s or 75s at 30 ⁇ L/min. Data was double-reference subtracted using both a surface without captured antibody and from injections of HBS-EP+ buffer. The equilibrium response was measured at 4 seconds before the end of association with a window of 5 seconds and fit using the Biacore T200 Evaluation Software 3.1 with the Steady State Affinity Model. The results are shown in Table 44. Table 44.
  • the binding kinetics of the EphA2 antibodies to the FN2 domain of hEphA2 [0435] Monovalent affinity to hEphA2-FN2 increased from ⁇ 2 ⁇ M from parental antibody AB- 008873 to ⁇ 20 nM for the engineered variant AB-010699. Binding of EphA2 antibodies to the FN2 domain of hEphA2 [0436] Binding of EphA2 antibodies to the FN2 domain of hEphA2 was measured using the Biacore ® T200 SPR system.
  • Biacore ® assays were conducted at 25°C using HBS-EP+ buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% v/v Surfactant P20) using the FN2 domain as the analyte with the antibodies in mIgG2a format as the immobilized ligand. Data was analyzed using 1:1 Langmuir binding model and steady-state model in Biacore Evaluation software. [0437] C-terminally His-tagged human EphA2 FN2 domain (Thr437-Asn534 + His tag) was used as the analyte. The analyte was associated for 120 seconds and dissociated for 100 seconds or 300 seconds at 30 ⁇ L/min.
  • Binding kinetics of for AB-010018 [0441] The calculated monovalent KD of AB-010699 is similar across all hEphA2 variants (ranging from 9 to 12 nM) and there appears to be no differentiated binding to different hEphA2 recombinant fragment representing cleavage forms (ranging from 9 to 12 nM). [0442] The calculated monovalent KD of AB-010018 is also similar across all hEphA2 variants (ranging from 6 to 11 nM) and there also appears to be no differentiated binding to different hEphA2 cleavage forms (ranging from 7 to 10 nM).
  • SCFVs Single-chain variable fragments (SCFVs) of 10699 were expressed with C-terminal His-tags in mammalian cells and purified by Nickel Sepharose affinity chromatography. SCFVs were assayed in triplicate for thermostability using an Unchained Labs UNcle instrument. The concentration of purified antibodies was adjusted to 0.5 mg/ml in PBS immediately prior to analysis. To determine melting temperature (Tm) intrinsic protein fluorescence was measured at 473 nm every 1.1°C as temperature was increased linearly from 25°C to 95°C at a rate of 0.3°C/min.
  • Tm melting temperature
  • the UNcle Analysis software (version 4.01) was used to find the Tm as the first derivative of the barycentric mean (BCM). Binding of the SCFVs to the FN2 domain of hEphA2 was measured in triplicate using the Biacore T200 SPR system at 25°C using HBS-EP+ buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% v/v Surfactant P20). SCFVs were captured at levels between 200-300 RU via an anti-His antibody immobilized to a CM5 chip.
  • Binding was assessed using a titration of FLAG-tagged hEphA2- FN2 (300 nM, 100 nM, 33 nM, 11 nM, 3.7 nM) associated for 120s and dissociated for 30s at 30 ⁇ L/min. Data was double-reference subtracted using both a surface without captured SCFV and from injections of HBS-EP+ buffer. The 1:1 Langmuir binding model was used to fit each titration and the average of three replicates is reported. Table 48 shows amino acid sequences in SCFV constructs, and the results are shown in Table 49. Table 48.
  • FIG. 32 shows schematics of the formats, including the format of the Fc regions. The constructs were tested for ADCC, and cell binding activity as described above. Certain of the tetravalent constructs tested exhibited improved ADCC and cell binding over the bivalent format. FIG.32 (RR) and Table 50. Those constructs that included components fused to the C-terminus of Fc exhibited substantial reduction of ADCC activity. Table 50. Tetravalent constructs
  • Receptor-linked interleukin-15 is made by covalently joining the IL-15 receptor alpha sushi domain to IL-15 via a glycine-serine linker.
  • RLI enables trans presentation of IL-15 to the IL-15 receptor complex (IL-15 receptor beta and IL-15 common gamma chain) on T and NK immune cells, and this trans presentation encourages immune responses such as proliferation and survival of na ⁇ ve CD8+ T cells, development of memory CD8+ T cells, improved survival and upregulation of lytic molecules and CD16a on NK cells, etc.
  • IL-15 MultiMabs Bispecific antibodies, referred to as IL-15 MultiMabs, that couple RLI to the anti-tumor antibody AB-008873 were developed.
  • IL-15 MultiMab a 2-plus-2 molecule (2p2) that links an RLI domain to the C-terminus of each light chain of an IgG molecule via a glycine-serine linker was created.
  • RLI domains can be either wildtype (“wt/RLI”) or a mutated variant expected to have lower affinity for the IL-15 receptor complex (“low/RLI”).
  • the two molecules described are shown here as FIG.36, and sequences of the component parts are provided in Table 15 above.
  • IL-15 MultiMabs have been assessed for their ability to induce proliferation of primary NK cells.
  • Primary human NK cells were labeled with CellTrace CFSE cell proliferation dye (Invitrogen Cat. C4554) and mixed with AB-008873 IL-15 MultiMabs. After 3 days of treatment, cells were analyzed with a flow cytometer and gated for cells that lost signal from proliferation dye relative to untreated cells. See FIG.37.
  • the AB-008873 IL-15 MultiMabs showed dose-dependent increases in human NK cell proliferation.
  • AB-008873 IL15 MultiMabs were assessed for their ability to bind to target tumor cells using flow cytometry. Parental antibody or IL-15 MultiMabs were added to CT26 ex vivo cells at 100 nM and incubated on ice, followed by washing. Secondary Alexa Fluor 647-conjugated anti-mouse antibody and cell membrane integrity dye was added and incubated on ice, followed by washing.
  • fusion proteins comprise (i) at least the antigen binding domains of the EphA2 antibodies and 4-1BB ligand domains (Table 13) or (ii) at least the antigen binding domains of the EphA2 antibodies and the ScFv portions of the anti-4-1BB antibodies (Table 10).
  • Bispecific antibodies that comprise two scFv fragments of anti-4-1BB antibody linked to the HC of the EphA2 antibodies AB-008873 or AB-010361 (EphA2-4-1BB bispecific antibodies) were constructed.
  • Anti-hen egg lysozyme targeting anti-4-1BB antibody (5554-41BB) was also constructed and used as a negative control.
  • EphA2-4-1BB bispecific antibodies were assayed for their ability to activate human 4-1BB using an inducible reporter cell system (Promega cat JA2351).4-1BB reporter cells were either cultured alone with the EphA2-4- 1BB bispecific antibodies or co-cultured with A549 tumor cells that had been treated with the EphA2- 4-1BB bispecific antibodies.
  • the 4-1BB antibody Urelumab (AB-009811) was included as a non-tumor targeting control. After 5 hours of culture, 4-1BB activation was determined from the reporter cells by measuring bioluminescence output.
  • the bispecific antibody that comprises two scFv fragments of anti-4-1BB antibody linked to the HC of the EphA2 antibody AB-010361 was tested in BALB/c mice that developed tumors after they have been inoculated with CT26 cells.
  • mice were dosed intraperitoneally with test article once a week for four weeks (7-, 14-, 21-, and 28-days post CT26 implantation) at a dose level of 10 mg/kg.
  • Vehicle control, PBS was dosed at 10 mL/kg.
  • mice treated with the EphA2-4-1BB bispecific antibody showed reduced tumor growth during the treatment period.
  • mice treated with the EphA2-4-1BB bispecific antibodies as above were assayed for the presence of liver toxicity, a known side effect of certain 4-1BB agonist-based therapeutics, including anti-4-1BB antibody Urelumab.
  • Liver toxicity was determined by measuring ALT (alanine aminotransferase) and AST (aspartate aminotransferase) which are released into the bloodstream when liver damage occurs.
  • the ALT was measured using the MAK052 assay kit (Sigma-Aldrich) which measures the amount of pyruvate generated and AST was measured using the MAK055 assay kits (Sigma-Aldrich) which measures the amount of glutamate generated.
  • mice treated with the AB-01361-4-1BB bispecific antibody and the AB-5554-41BB negative control do not show increase over vehicle of ALT & AST levels while the antibody 3H3 at 10 mg/kg (mouse surrogate for Urelumab) shows increased serum ALT & AST levels (ALT ⁇ 8-fold increase, p ⁇ 0.0001).
  • livers from mice treated with the AB-01361-4-1BB bispecific antibody showed no visible signs of liver inflammation as determined by tissue staining using hematoxylin and eosin.
  • Portal vein infiltration and expansion to parenchyma was detected with 10 mpk 3H3 but not AB-010361-41BB.
  • CD3 BISPECIFIC CONSTRUCTS This example describes CD3 bispecific antibodies comprising the anti-tumor antibodies described herein.
  • Table 9 provides specific examples of anti-CD3 binding arms that can be combined with any of the anti-EphA2 antibodies described herein.
  • Fig. 53 provides examples of anti-EphA2/ anti-CD3 bispecific constructs that can be generated.
  • Bispecific constructs generated using a 1+1 format with the CD3 arm comprising the VH/VL sequence of AB-008707 were assayed for in vivo activity in a mouse model as follows. NSG-DKO mice were inoculated subcutaneously in the flank with 5e6 PC3 tumor cells in 50% matrigel on Day 0.
  • mice Human PBMCs from three individual donors were engrafted via IV tail vein injection on day 1 following inoculation (10e6 cells/mouse). Mice were randomized into 5 mice per group per donor based on tumor volume and treated with either vehicle, 5 mg/kg anti-hen egg lysozyme non-targeting control 5554/CD3, 5 mg/kg AB-010361/CD3, or 1 mg/kg cetuximab/CD3 positive control intraperitoneally 1x/week for 3 weeks (indicated by the dotted vertical lines). Tumor volumes were measured twice per week until mice were euthanized.
  • ADC CONSTRUCTS ADC in vitro [0464] This experiment tested the cytotoxicity of antibody-drug conjugates (“conjugates”) each comprising an EphA2 antibody directly conjugated via a lysine to a ZymeLinkTM Auristatin (ZLA) payload having structure (1) as disclosed above on SKOV3, MDAMB231, and PC3 tumor cells.
  • conjugates each comprising an EphA2 antibody directly conjugated via a lysine to a ZymeLinkTM Auristatin (ZLA) payload having structure (1) as disclosed above on SKOV3, MDAMB231, and PC3 tumor cells.
  • ZLA ZymeLinkTM Auristatin
  • Each of the ADCs has Formula (I).
  • the average drug to antibody ratio (DAR) for each molecule ranges from 2.9 and 3.6 as determined by Mass Spectrometry.
  • EphA2 antibodies assessed include AB-010361 (IgG1), AB-10699 (IgG1), AB-010361 (IgG4), and AB-010671 (IgG1) and their conjugates are shown as “AB-0010361-ZLA,” “AB-010699-ZLA,” “AB-010361-ZLA-IgG4,” and “AB-010671-ZLA” in FIG. 55A-D.
  • Target tumor cells were detached from the culture plate and cell concentration was adjusted to 31,250 cells/mL in assay media.2,500 cells were added to each well of a 96 well plate and incubated with different concentrations of directly conjugated primary antibody for 15 min at room temperature. Cells were then incubated for 72h at 37 ⁇ C and 5% CO2.
  • FIG.59B In vivo PC3 model
  • This experiment assessed the activity of ZLA-Conjugated EphA2 antibodies AB-010671- ZLA and AB-010699-ZLA in vivo.
  • 2x10 6 PC3 cells were inoculated in 0.2 mL of 1:1 DPBS with Matrigel subcutaneously into each of the male NPG mice. Tumors were allowed to establish and then randomized at an average size of 150 mm 3 with 10 mice per treatment cohort. Treatment started at the day of randomization (Day 0) with weekly intravenous injections of the conjugates at the indicated doses. Body weight as well as tumor sizes were monitored twice weekly. Study was ended at day 35 after 5 doses.
  • mice were euthanized, and tumors excised and weighted.
  • the results showed that AB-010671-ZLA (FIG 56C and AB-010699-ZLA (FIG 56D) exhibited dose dependent anti-tumor activity with significant tumor reduction over isotype-ZLA observed at 3 and 6 mg/kg.
  • AB-010361-ZLA and AB-010361-IgG4-ZLA showed weak activity at the highest dose tested (FIG 56A and 56B) with AB-010361-IgG4-ZLA being more efficacious as AB- 010361-ZLA.
  • This tumor size observation is confirmed by endpoint tumor weight analysis (FIG 57).
  • AB-016699-ZLA and AB-010671-ZLA showed significantly smaller tumors in mice dosed with the conjugates at 3 mg/kg and 6 mg/kg whereas AB-010361-IgG4-ZLA showed significantly smaller tumors at 6 mg/kg.
  • Body weights were measured throughout the study and inversely correlated with tumor burden (FIG 58). Weight loss occurred in mice towards the end of the study starting from day 28 and was most prominent for vehicle and isotype control groups as well as tumors who didn’t respond to therapy as outlined above.
  • the assay was repeated with AB-010699 and AB-010671 in both IgG1 and IgG4 formats at 1, 3, and 6 mg/kg, AB-010016, and vehicle and isotype controls in mice carrying PC3 tumor cells measuring ⁇ 150 mm 3 or ⁇ 400 mm 3 .
  • AB-010699 and AB-010671 in both IgG1 and IgG4 formats showed anti-tumor activity at 3 and 6 mg/kg in both the ⁇ 150 mm 3 (FIG.60A) and the larger more established tumor models (FIG.61A), with AB-010699-IgG4 exhibiting slightly better efficacy compared to AB- 010671-IgG4.
  • FIG.60B and FIG.61B show the body weight of the mice over the course of the studies.

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Abstract

L'invention concerne un immunoconjugué comprenant un anticorps qui se lie au récepteur de l'éphrine A2 (EphA2) et un agent cytotoxique. L'agent cytotoxique est un analogue d'auristatine, et l'anticorps est conjugué à l'analogue d'auristatine. Ces immunoconjugués comprenant des anticorps anti-EphA2 se lient de préférence à un tissu tumoral par rapport à un tissu normal, et ils peuvent être utilisés dans des procédés d'induction d'une réponse immunitaire et des procédés d'inhibition de la croissance de cellules tumorales.
PCT/US2023/065395 2022-04-05 2023-04-05 Anticorps anti-epha2 WO2023196869A1 (fr)

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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170267768A1 (en) * 2016-03-16 2017-09-21 The Regents Of The University Of California Protein A Binding Polypeptides, Anti-EphA2 Antibodies and Methods of Use Thereof
WO2021003399A1 (fr) * 2019-07-03 2021-01-07 Iconic Therapeutics, Inc. Conjugués anticorps anti-facteur tissulaire-médicament et méthodes associées

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170267768A1 (en) * 2016-03-16 2017-09-21 The Regents Of The University Of California Protein A Binding Polypeptides, Anti-EphA2 Antibodies and Methods of Use Thereof
WO2021003399A1 (fr) * 2019-07-03 2021-01-07 Iconic Therapeutics, Inc. Conjugués anticorps anti-facteur tissulaire-médicament et méthodes associées

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HASEGAWA JUN, SUE MAYUMI, YAMATO MICHIKO, ICHIKAWA JUNYA, ISHIDA SAORI, SHIBUTANI TOMOKO, KITAMURA MICHIKO, WADA TEIJI, AGATSUMA T: "Novel anti-EPHA2 antibody, DS-8895a for cancer treatment", CANCER BIOLOGY & THERAPY, LANDES BIOSCIENCE, US, vol. 17, no. 11, 1 November 2016 (2016-11-01), US , pages 1158 - 1167, XP093102496, ISSN: 1538-4047, DOI: 10.1080/15384047.2016.1235663 *

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